| Author | Title | Year | Journal/Proceedings | Reftype | DOI/URL |
|---|---|---|---|---|---|
| Copley, S.D., Smith, E., Morowitz, H.J. and Petsko, G.A. | A Mechanism for the Association of Amino Acids with Their Codons and the Origin of the Genetic Code | 2005 | Proceedings of the National Academy of Sciences of the United States of America Vol. 102(12), pp. 4442-4447 |
article | URL |
| Abstract: The genetic code has certain regularities that have resisted mechanistic interpretation. These include strong correlations between the first base of codons and the precursor from which the encoded amino acid is synthesized and between the second base of codons and the hydrophobicity of the encoded amino acid. These regularities are even more striking in a projection of the modern code onto a simpler code consisting of doublet codons encoding a set of simple amino acids. These regularities can be explained if, before the emergence of macromolecules, simple amino acids were synthesized in covalent complexes of dinucleotides with α-keto acids originating from the reductive tricarboxylic acid cycle or reductive acetate pathway. The bases and phosphates of the dinucleotide are proposed to have enhanced the rates of synthetic reactions leading to amino acids in a small-molecule reaction network that preceded the RNA translation apparatus but created an association between amino acids and the first two bases of their codons that was retained when translation emerged later in evolution.; The genetic code has certain regularities that have resisted mechanistic interpretation. These include strong correlations between the first base of codons and the precursor from which the encoded amino acid is synthesized and between the second base of codons and the hydrophobicity of the encoded amino acid. These regularities are even more striking in a projection of the modern code onto a simpler code consisting of doublet codons encoding a set of simple amino acids. These regularities can be explained if, before the emergence of macromolecules, simple amino acids were synthesized in covalent complexes of dinucleotides with alpha-keto acids originating from the reductive tricarboxylic acid cycle or reductive acetate pathway. The bases and phosphates of the dinucleotide are proposed to have enhanced the rates of synthetic reactions leading to amino acids in a small-molecule reaction network that preceded the RNA translation apparatus but created an association between amino acids and the first two bases of their codons that was retained when translation emerged later in evolution. [PUBLICATION ABSTRACT]; The genetic code has certain regularities that have resisted mechanistic interpretation. These include strong correlations between the first base of codons and the precursor from which the encoded amino acid is synthesized and between the second base of codons and the hydrophobicity of the encoded amino acid. These regularities are even more striking in a projection of the modern code onto a simpler code consisting of doublet codons encoding a set of simple amino acids. These regularities can be explained if, before the emergence of macromolecules, simple amino acids were synthesized in covalent complexes of dinucleotides with alpha-keto acids originating from the reductive tricarboxylic acid cycle or reductive acetate pathway. The bases and phosphates of the dinucleotide are proposed to have enhanced the rates of synthetic reactions leading to amino acids in a small-molecule reaction network that preceded the RNA translation apparatus but created an association between amino acids and the first two bases of their codons that was retained when translation emerged later in evolution.; The genetic code has certain regularities that have resisted mechanistic interpretation. These include strong correlations between the first base of codons and the precursor from which the encoded amino acid is synthesized and between the second base of codons and the hydrophobicity of the encoded amino acid. These regularities are even more striking in a projection of the modern code onto a simpler code consisting of doublet codons encoding a set of simple amino acids. These regularities can be explained if, before the emergence of macromolecules, simple amino acids were synthesized in covalent complexes of dinucleotides with alpha-keto acids originating from the reductive tricarboxylic acid cycle or reductive acetate pathway. The bases and phosphates of the dinucleotide are proposed to have enhanced the rates of synthetic reactions leading to amino acids in a small-molecule reaction network that preceded the RNA translation apparatus but created an association between amino acids and the first two bases of their codons that was retained when translation emerged later in evolution.; The genetic code has certain regularities that have resisted mechanistic interpretation. These include strong correlations between the first base of codons and the precursor from which the encoded amino acid is synthesized and between the second base of codons and the hydrophobicity of the encoded amino acid. These regularities are even more striking in a projection of the modern code onto a simpler code consisting of doublet codons encoding a set of simple amino acids. These regularities can be explained if, before the emergence of macromolecules, simple amino acids were synthesized in covalent complexes of dinucleotides with α-keto acids originating from the reductive tricarboxylic acid cycle or reductive acetate pathway. The bases and phosphates of the dinucleotide are proposed to have enhanced the rates of synthetic reactions leading to amino acids in a small-molecule reaction network that preceded the RNA translation apparatus but created an association between amino acids and the first two bases of their codons that was retained when translation emerged later in evolution. catalysis origin of life; The genetic code has certain regularities that have resisted mechanistic interpretation. These include strong correlations between the first base of codons and the precursor from which the encoded amino acid is synthesized and between the second base of codons and the hydrophobicity of the encoded amino acid. These regularities are even more striking in a projection of the modern code onto a simpler code consisting of doublet codons encoding a set of simple amino acids. These regularities can be explained if, before the emergence of macromolecules, simple amino acids were synthesized in covalent complexes of dinucleotides with [alpha]-keto acids originating from the reductive tricarboxylic acid cycle or reductive acetate pathway. The bases and phosphates of the dinucleotide are proposed to have enhanced the rates of synthetic reactions leading to amino acids in a small-molecule reaction network that preceded the RNA translation apparatus but created an association between amino acids and the first two bases of their codons that was retained when translation emerged later in evolution.; The genetic code has certain regularities that have resisted mechanistic interpretation. These include strong correlations between the first base of codons and the precursor from which the encoded amino acid is synthesized and between the second base of codons and the hydrophobicity of the encoded amino acid. These regularities are even more striking in a projection of the modern code onto a simpler code consisting of doublet codons encoding a set of simple amino acids. These regularities can be explained if, before the emergence of macromolecules, simple amino acids were synthesized in covalent complexes of dinucleotides with α-keto acids originating from the reductive tricarboxylic acid cycle or reductive acetate pathway. The bases and phosphates of the dinucleotide are proposed to have enhanced the rates of synthetic reactions leading to amino acids in a small-molecule reaction network that preceded the RNA translation apparatus but created an association between amino acids and the first two bases of their codons that was retained when translation emerged later in evolution. | |||||
BibTeX:
@article{copley_mechanism_2005,
author = {Copley, Shelley D. and Smith, Eric and Morowitz, Harold J. and Petsko, Gregory A.},
title = {A Mechanism for the Association of Amino Acids with Their Codons and the Origin of the Genetic Code},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2005},
volume = {102},
number = {12},
pages = {4442--4447},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3db9MwED8hQAgJIQpbFj4kI8E0HpoltlM7D3uYBtMkeASJN8txHFGpTcuSvfDXc-ck7VqGhHip5PpsOb7z-Wzf_Q5A8CSd7ukEr9zMilklFfeyKp0oBWpOKVyRp3Wp9m62YXx3JyfLHVfFpJn_CO6Ww7xeh3xrSU3nRvqrOsvJ7Uofd6vV4my9DM38r-OeLuAQ2ZLuEFyHapvg0sYD_ganV_dRKxyVt-RyRANS4nTd2DZJczrA4B4b0uCgsS4VZaa8tacNmr33biTIVGx2l_n6pxfmQwpEuWnv3ALDdnf5DJ4Odio77ydgAvd88xwmgyZo2ckAV_3hBbhztvQUPzxvlwxNYIYmJbNbrrNVzexy3qyYdfOqZXTzy8L7BHN4Jm5aZpsqNOqTdBE9lVCyKcCSiPwBfLv89PXiajqkbpg6qYsMfyuBRy8uq3TmJLde65p0K904FXWa2TJVyH6ec1cXqnC6dEpb5a11hauEE4fwxJKLf9OFUMAqggc1rkcf0R4Z4XRE8Oh78eWjvvp80RcnYzFpQ7xa8rOLkKthOU9niToCprwveeZUVlsruct0kdrS6hoFpq5wpDGcjHw06x7sw4RHeiUMsdFsuR9DRHw2pAZInEwmyGFQKxHDQWD9pgch0CpLsxiOQh_bjrnJuJFSYmdv_1Zl6sEHKIbDUYRMtVgYTV6Fhcqx36iXo23zQSxjmO1I2IaAIMV3a3BZBWjxfvXE8L4XxU0LblpucCZyHBOlKFCp6WhM0R6dpDHhVMTw7rYMb-oD3pLSBDJISG8xZP9CdjHA1RNMQ_fyf7_qFTwOuLupmHL-Gu531zf-TY—RuSEmtu}
}
|
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| Ubriaco, M.R. | A simple mathematical model for anomalous diffusion via Fisher's information theory | 2009 | Physics Letters A Vol. 373(44), pp. 4017-4021 |
article | |
| Abstract: Starting with the relative entropy based on a previously proposed entropy function S.sub.q[p]=a'dxp(x)x(-lnp(x)).sup.q, we find the corresponding Fisher's information measure. After function redefinition we then maximize the Fisher information measure with respect to the new function and obtain a differential operator that reduces to a space coordinate second derivative in the q[right arrow]1 limit. We then propose a simple differential equation for anomalous diffusion and show that its solutions are a generalization of the functions in the Barenblatt-Pattle solution. We find that the mean squared displacement, up to a q-dependent constant, has a time dependence according to (x.sup.2)[approximately equal to]K.sup.1/qt.sup.1/q, where the parameter q takes values q=2n-1/2n+1 (superdiffusion) and q=2n+1/2n-1 (subdiffusion), an[greater than or equal to]1.;Starting with the relative entropy based on a previously proposed entropy function Sq[p]=ınt dx p(x)(-\ln p(x))textasciicircumq, we find the corresponding Fisher's information measure. After function redefinition we then maximize the Fisher information measure with respect to the new function and obtain a differential operator that reduces to a space coordinate second derivative in the q\to 1 limit. We then propose a simple differential equation for anomalous diffusion and show that its solutions are a generalization of the functions in the Barenblatt-Pattle solution. We find that the mean squared displacement, up to a q-dependent constant, has a time dependence according to textlessxtextasciicircum2textgreater\sim Ktextasciicircum1/qttextasciicircum1/q, where the parameter q takes values q=\frac2n-12n+1 (superdiffusion) and q=\frac2n+12n-1 (subdiffusion), \forall n\geq 1.;Starting with the relative entropy based on a previously proposed entropy function S [p] = ∫ d x p (x) × (- ln p (x)) , we find the corresponding Fisher's information measure. After function redefinition we then maximize the Fisher information measure with respect to the new function and obtain a differential operator that reduces to a space coordinate second derivative in the q → 1 limit. We then propose a simple differential equation for anomalous diffusion and show that its solutions are a generalization of the functions in the Barenblatt-Pattle solution. We find that the mean squared displacement, up to a q-dependent constant, has a time dependence according to 〈 x 〉 ∼ K t , where the parameter q takes values q = frac(2 n - 1, 2 n + 1) (superdiffusion) and q = frac(2 n + 1, 2 n - 1) (subdiffusion), ∀ n ≥ 1. © 2009 Elsevier B.V. All rights reserved.;Starting with the relative entropy based on a previously proposed entropy function S-q vertical bar P vertical bar = integral dx p(x) x (-In p(x))(q), we find the corresponding Fisher's information measure. After function redefinition we then maximize the Fisher information measure with respect to the new function and obtain a differential operator that reduces to a space coordinate second derivative in the q 1 limit. We then propose a simple differential equation for anomalous diffusion and show that its solutions are a generalization or the functions in the Barenblatt-Pattie solution. We find that the mean squared displacement, Lip to a q-dependent constant, has a time dependence according to textless x(2)textgreater similar to K(1/q)t(1/q), where the parameter q takes values q = 2n-1/sn+1 (superdiffusion) and q = 2n+1/2n-1 (subdiffusion), for all n textgreater= 1. (C) 2009 Elsevier B.V. All rights reserved.; | |||||
BibTeX:
@article{ubriaco_simple_2009,
author = {Ubriaco, Marcelo R.},
title = {A simple mathematical model for anomalous diffusion via Fisher's information theory},
journal = {Physics Letters A},
year = {2009},
volume = {373},
number = {44},
pages = {4017--4021}
}
|
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| Chaitin, G. | A Theory of Program Size Formally Identical to Information Theory [BibTeX] |
1975 | Journal of the ACM (JACM) Vol. 22(3), pp. 329-340 |
article | |
BibTeX:
@article{chaitin_theory_1975,
author = {Chaitin, Gregory},
title = {A Theory of Program Size Formally Identical to Information Theory},
journal = {Journal of the ACM (JACM)},
year = {1975},
volume = {22},
number = {3},
pages = {329--340}
}
|
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| Joyce, P., Rokyta, D.R., Wichman, H.A. and Caudle, S.B. | An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus | 2005 | Nature genetics Vol. 37(4), pp. 441-444 |
article | URL |
| Abstract: The primary impediment to formulating a general theory for adaptive evolution has been the unknown distribution of fitness effects for new beneficial mutations. By applying extreme value theory, Gillespie circumvented this issue in his mutational landscape model for the adaptation of DNA sequences, and Orr recently extended Gillespie's model, generating testable predictions regarding the course of adaptive evolution. Here we provide the first empirical examination of this model, using a single-stranded DNA bacteriophage related to X174, and find that our data are consistent with Orr's predictions, provided that the model is adjusted to incorporate mutation bias. Orr's work suggests that there may be generalities in adaptive molecular evolution that transcend the biological details of a system, but we show that for the model to be useful as a predictive or inferential tool, some adjustments for the biology of the system will be necessary.; The primary impediment to formulating a general theory for adaptive evolution has been the unknown distribution of fitness effects for new beneficial mutations(1). By applying extreme value theory(2), Gillespie circumvented this issue in his mutational landscape model for the adaptation of DNA sequences(3-5), and Orr recently extended Gillespie's model(1,6), generating testable predictions regarding the course of adaptive evolution. Here we provide the first empirical examination of this model, using a single-stranded DNA bacteriophage related to phi X174, and find that our data are consistent with Orr's predictions, provided that the model is adjusted to incorporate mutation bias. Orr's work suggests that there may be generalities in adaptive molecular evolution that transcend the biological details of a system, but we show that for the model to be useful as a predictive or inferential tool, some adjustments for the biology of the system will be necessary.; The primary impediment to formulating a general theory for adaptive evolution has been the unknown distribution of fitness effects for new beneficial mutations. By applying extreme value theory, Gillespie circumvented this issue in his mutational landscape model for the adaptation of DNA sequences, and Orr recently extended Gillespie's model, generating testable predictions regarding the course of adaptive evolution. Here we provide the first empirical examination of this model, using a single-stranded DNA bacteriophage related to phiX174, and find that our data are consistent with Orr's predictions, provided that the model is adjusted to incorporate mutation bias. Orr's work suggests that there may be generalities in adaptive molecular evolution that transcend the biological details of a system, but we show that for the model to be useful as a predictive or inferential tool, some adjustments for the biology of the system will be necessary.; The primary impediment to formulating a general theory for adaptive evolution has been the unknown distribution of fitness effects for new beneficial mutations. By applying extreme value theory, Gillespie circumvented this issue in his mutational landscape model for the adaptation of DNA sequences, and Orr recently extended Gillespie's model, generating testable predictions regarding the course of adaptive evolution. Here we provide the first empirical examination of this model, using a single-stranded DNA bacteriophage related to phiX174, and find that our data are consistent with Orr's predictions, provided that the model is adjusted to incorporate mutation bias. Orr's work suggests that there may be generalities in adaptive molecular evolution that transcend the biological details of a system, but we show that for the model to be useful as a predictive or inferential tool, some adjustments for the biology of the system will be necessary. | |||||
BibTeX:
@article{joyce_empirical_2005,
author = {Joyce, Paul and Rokyta, Darin R. and Wichman, Holly A. and Caudle, S. B.},
title = {An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus},
journal = {Nature genetics},
year = {2005},
volume = {37},
number = {4},
pages = {441--444},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3BbtQwEB0BFQgJAYU2BKjwAY7ZbmzHTk5o2VJVAnHqobfIjb2rStvdtEkQ_D0zdpJ2C0iIUxTZshxnPPPsmXkDIPhkmtzRCalQJk0pDbLgTuVKaqps5tCY5ZoLa7dvtmFghej_9qAkvea2m4ouzQ_RsCmNcEZ-rK8SqiJF3ta-pMZ92EkpKxXlW599Gr0KVF3Zez8VnZvIbRlqDYn8cL3ErZ9tGadeRW8zbG4hUKIXrTZ11_zRankLdfwMhpCpITJldFffJNT_Hrn9v1_-HJ72SJbNgujtwj23fgEPQ23Lny-hmq2Zu6wvPAUJQ0Dbss2CIdxkl13b30Ayn2hMIVjMV-ShHsaaOrQzislfMsPosXIJXcrQfT07-jZj3y-uu2YPTo8_n85Pkr6iQ1JxoaZJZfEwbg0XsjAIBIVCfKEX58XUOKeFQf2RZq5A0JVrm-NhC9EUN5oqahlJhdr34YmhwP916xMEbQQ7C9ylLiLLGeGKR_DorPh6lJ98mYfX3eF10vgstslVG6E4-LVK1ES_ApaiIFprTFahbsrPeSG5ydKKqN8yBMcihneDUJR1oAApvete5GUQmxgOSFZK4tNYU8DO0nRNU6K2lCkeEWUMUd–2OBSVbdb9oJ4jSMPI0bDry_takXM0giFcQel1OKF72YuOEvUujqGD0EaxxZeNrzEmapcSqEKxLJl-6PFEe70k-T-xQ0Zw_vbYjy296xJ0p8oxTSG9F-6zXuSeSJXaF__9YPewGNPh-ujod7Cg_a6cweBFPMXUURD0Q}
}
|
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| Millikan, R.G. | An Input Condition for Teleosemantics? Reply to Shea (And Godfrey-Smith) [BibTeX] |
2007 | Philosophy and Phenomenological Research Vol. 75(2), pp. 436-455 |
article | URL |
BibTeX:
@article{millikan_input_2007,
author = {Millikan, Ruth G.},
title = {An Input Condition for Teleosemantics? Reply to Shea (And Godfrey-Smith)},
journal = {Philosophy and Phenomenological Research},
year = {2007},
volume = {75},
number = {2},
pages = {436--455},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1bS8MwFA7i00C8D-cF8uCDPlTbtE3SpzGGOt-GzOeSW0GY7XQduH_vSXpxGwrzrdBbmnOa8yXny3cQCsmd722MCYprw6lWgZQq85XgJrMpKojGiYm4E99fWdluVzIsydKxBF1OH-CSnJp763Xwh9L-7MOz1aNslrUupQFDcQCIpNLJbQdk5ge1OmPgQcCL10JQxULcCDvrSNWFmscD1HDbGopJm3f-2Rn_CwX7n59wiPZrKIoHle8coR2TH6POuKltsDxBo0GOn_PZosTDwqa2wYYYQC6eQKwq5uYdrPKm5n0MKH66xGWBbX1sfDPINX4qtN0h5rmVm9tT9Pr4MBmOvLr0gqcAAoaelIQZrQXgGyUCxhQlRhCTSMZiKYzhEfEjJbKEciGlYLFQLBIxybSOJFVJ2EV7wlL0bTsANOszhElmTMa5seLIETxBhJJLQCvgFNpQmvVQ0JglnVVSG-nKFCUJwxSwF7GFM13OnIfpVw91Xee2NzQ920PXqwZtz_uVaBvMEh06hnduc9mw1ku3OgFlD1HnHFs3Mh2Pxi9wdP5XYy9Qp1oyttS1S7Rbfi7MVaUL-Q0UuPyq}
}
|
|||||
| Artmann, S. | Biological Information [BibTeX] |
2008 | , pp. 22-39 | incollection | |
BibTeX:
@incollection{artmann_biological_2008,
author = {Artmann, Stefan},
title = {Biological Information},
year = {2008},
pages = {22--39}
}
|
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| Galas, D.J., Nykter, M., Carter, G.W., Price, N.D. and Shmulevich, I. | Biological Information as Set-Based Complexity | 2010 | IEEE Transactions on Information Theory Vol. 56(2), pp. 667-677 |
article | URL |
| Abstract: The significant and meaningful fraction of all the potential information residing in the molecules and structures of living systems is unknown. Sets of random molecular sequences or identically repeated sequences, for example, would be expected to contribute little or no useful information to a cell. This issue of quantitation of information is important since the ebb and flow of biologically significant information is essential to our quantitative understanding of biological function and evolution. Motivated specifically by these problems of biological information, a class of measures is proposed to quantify the contextual nature of the information in sets of objects, based on Kolmogorov's intrinsic complexity. Such measures discount both random and redundant information and are inherent in that they do not require a defined state space to quantify the information. The maximization of this new measure, which can be formulated in terms of the universal information distance, appears to have several useful and interesting properties, some of which we illustrate with examples.; The significant and meaningful fraction of all the potential information residing in the molecules and structures of living systems is unknown. Sets of random molecular sequences or identically repeated sequences, for example, would be expected to contribute little or no useful information to a cell. This issue of quantitation of information is important since the ebb and flow of biologically significant information is essential to our quantitative understanding of biological function and evolution. Motivated specifically by these problems of biological information, a class of measures is proposed to quantify the contextual nature of the information in sets of objects, based on Kolmogorov's intrinsic complexity. Such measures discount both random and redundant information and are inherent in that they do not require a defined state space to quantify the information. The maximization of this new measure, which can be formulated in terms of the universal information distance, appears to have several useful and interesting properties, some of which we illustrate with examples. [PUBLICATION ABSTRACT]; The significant and meaningful fraction of all the potential information residing in the molecules and structures of living systems is unknown. Sets of random molecular sequences or identically repeated sequences, for example, would be expected to contribute little or no useful information to a cell. This issue of quantitation of information is important since the ebb and flow of biologically significant information is essential to our quantitative understanding of biological function and evolution. Motivated specifically by these problems of biological information, a class of measures is proposed to quantify the contextual nature of the information in sets of objects, based on Kolmogorov's intrinsic complexity. Such measures discount both random and redundant information and are inherent in that they do not require a defined state space to quantify the information. The maximization of this new measure, which can be formulated in terms of the universal information distance, appears to have several useful and interesting properties, some of which we illustrate with examples.; The significant and meaningful fraction of all the potential information residing in the molecules and structures of living systems is unknown. Sets of random molecular sequences or identically repeated sequences, for example, would be expected to contribute little or no useful information to a cell. This issue of quantitation of information is important since the ebb and flow of biologically significant information is essential to our quantitative understanding of biological function and evolution. Motivated specifically by these problems of biological information, a class of measures is proposed to quantify the contextual nature of the information in sets of objects, based on Kolmogorov's intrinsic complexity. Such measures discount both random and redundant information and are inherent in that they do not require a defined state space to quantify the information. The maximization of this new measure, which can be formulated in terms of the universal information distance, appears to have several useful and interesting properties, some of which we illustrate with examples. [PUBLICATION ABSTRACT] | |||||
BibTeX:
@article{galas_biological_2010,
author = {Galas, D. J. and Nykter, M. and Carter, G. W. and Price, N. D. and Shmulevich, I.},
title = {Biological Information as Set-Based Complexity},
journal = {IEEE Transactions on Information Theory},
year = {2010},
volume = {56},
number = {2},
pages = {667--677},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1Lb9QwEB4hDgiEKC2QBlopBzhwSOpX1vERFqoiuLFI3CzHdk6rim5SCf49M3GSLgUJxC1WEufhsecbz8w3AFJUrLy1JpiuFSq0rUM87lqpUU37RnucXExqN-5k7O1sw1xlkeqdjKFosaLD0bOP7f7Mtb112-1IK-h2U_GMWqElb8h-51zzlMu1eBRUzRNzOMcJjjbJ7LJk5mzzYZOIKwW-DCMovKeipoV6LL3yKwqltJHr_o8Ka1RO5wcwO6rnoJTFU32TS_970PZ_ffRjeDQh2OJNErlDuBMvj-Bgrg5RTIvFETzYozp8AlUqekkiUUwpUCQSheuLz3Eo36IyDQV1QgSdw4-n8OX8_WZ9UU61Gkqv0IQpZSs77jpc-bmXwQlBpDLMeRGCkFE0HVMy-M4Z3fFoePBy1arQNa1Gg8rVWj6Dh45i-i-HMfcvZHB32F3HjHRihj80g3tfzad3zcXHdWoezs2qH_PTqqshw8Eep2-5qvQxFIGjgHpfy66RKnqBDzMympY1IaIZVefweh5o-y2Re9jRKGLGolBQiU5jJ6HIISNJsDTvh53zViBYQuzIRA6nNE5LD2wE3ivVcB6iiTGHk1lqLA4h3Tz0lkh9EAsqgx0vp8N2iycaskm15jm8SjK2dC1sLyyzWq8U4m78dcoO34ccjm9dJ2vEvabhKoeX-9J58460HVEzKahmLJM58H-5bD3RxhNdwvD8L5_9Au6nSAvarjpJo3mayC5_AthzNuc}
}
|
|||||
| Galas, D.J., Nykter, M., Carter, G.W., Price, N.D. and Shmulevich, I. | Biological Information as Set-Based Complexity | 2010 | IEEE Transactions on Information Theory Vol. 56(2), pp. 667-677 |
article | URL |
| Abstract: The significant and meaningful fraction of all the potential information residing in the molecules and structures of living systems is unknown. Sets of random molecular sequences or identically repeated sequences, for example, would be expected to contribute little or no useful information to a cell. This issue of quantitation of information is important since the ebb and flow of biologically significant information is essential to our quantitative understanding of biological function and evolution. Motivated specifically by these problems of biological information, a class of measures is proposed to quantify the contextual nature of the information in sets of objects, based on Kolmogorov's intrinsic complexity. Such measures discount both random and redundant information and are inherent in that they do not require a defined state space to quantify the information. The maximization of this new measure, which can be formulated in terms of the universal information distance, appears to have several useful and interesting properties, some of which we illustrate with examples.; The significant and meaningful fraction of all the potential information residing in the molecules and structures of living systems is unknown. Sets of random molecular sequences or identically repeated sequences, for example, would be expected to contribute little or no useful information to a cell. This issue of quantitation of information is important since the ebb and flow of biologically significant information is essential to our quantitative understanding of biological function and evolution. Motivated specifically by these problems of biological information, a class of measures is proposed to quantify the contextual nature of the information in sets of objects, based on Kolmogorov's intrinsic complexity. Such measures discount both random and redundant information and are inherent in that they do not require a defined state space to quantify the information. The maximization of this new measure, which can be formulated in terms of the universal information distance, appears to have several useful and interesting properties, some of which we illustrate with examples. [PUBLICATION ABSTRACT]; The significant and meaningful fraction of all the potential information residing in the molecules and structures of living systems is unknown. Sets of random molecular sequences or identically repeated sequences, for example, would be expected to contribute little or no useful information to a cell. This issue of quantitation of information is important since the ebb and flow of biologically significant information is essential to our quantitative understanding of biological function and evolution. Motivated specifically by these problems of biological information, a class of measures is proposed to quantify the contextual nature of the information in sets of objects, based on Kolmogorov's intrinsic complexity. Such measures discount both random and redundant information and are inherent in that they do not require a defined state space to quantify the information. The maximization of this new measure, which can be formulated in terms of the universal information distance, appears to have several useful and interesting properties, some of which we illustrate with examples.; The significant and meaningful fraction of all the potential information residing in the molecules and structures of living systems is unknown. Sets of random molecular sequences or identically repeated sequences, for example, would be expected to contribute little or no useful information to a cell. This issue of quantitation of information is important since the ebb and flow of biologically significant information is essential to our quantitative understanding of biological function and evolution. Motivated specifically by these problems of biological information, a class of measures is proposed to quantify the contextual nature of the information in sets of objects, based on Kolmogorov's intrinsic complexity. Such measures discount both random and redundant information and are inherent in that they do not require a defined state space to quantify the information. The maximization of this new measure, which can be formulated in terms of the universal information distance, appears to have several useful and interesting properties, some of which we illustrate with examples. [PUBLICATION ABSTRACT] | |||||
BibTeX:
@article{galas_biological_2010,
author = {Galas, D. J. and Nykter, M. and Carter, G. W. and Price, N. D. and Shmulevich, I.},
title = {Biological Information as Set-Based Complexity},
journal = {IEEE Transactions on Information Theory},
year = {2010},
volume = {56},
number = {2},
pages = {667--677},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1Lb9QwEB4hDgiEKC2QBlopBzhwSOpX1vERFqoiuLFI3CzHdk6rim5SCf49M3GSLgUJxC1WEufhsecbz8w3AFJUrLy1JpiuFSq0rUM87lqpUU37RnucXExqN-5k7O1sw1xlkeqdjKFosaLD0bOP7f7Mtb112-1IK-h2U_GMWqElb8h-51zzlMu1eBRUzRNzOMcJjjbJ7LJk5mzzYZOIKwW-DCMovKeipoV6LL3yKwqltJHr_o8Ka1RO5wcwO6rnoJTFU32TS_970PZ_ffRjeDQh2OJNErlDuBMvj-Bgrg5RTIvFETzYozp8AlUqekkiUUwpUCQSheuLz3Eo36IyDQV1QgSdw4-n8OX8_WZ9UU61Gkqv0IQpZSs77jpc-bmXwQlBpDLMeRGCkFE0HVMy-M4Z3fFoePBy1arQNa1Gg8rVWj6Dh45i-i-HMfcvZHB32F3HjHRihj80g3tfzad3zcXHdWoezs2qH_PTqqshw8Eep2-5qvQxFIGjgHpfy66RKnqBDzMympY1IaIZVefweh5o-y2Re9jRKGLGolBQiU5jJ6HIISNJsDTvh53zViBYQuzIRA6nNE5LD2wE3ivVcB6iiTGHk1lqLA4h3Tz0lkh9EAsqgx0vp8N2iycaskm15jm8SjK2dC1sLyyzWq8U4m78dcoO34ccjm9dJ2vEvabhKoeX-9J58460HVEzKahmLJM58H-5bD3RxhNdwvD8L5_9Au6nSAvarjpJo3mayC5_AthzNuc}
}
|
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| Akay, M. | Biomedical signal processing [BibTeX] |
2012 | book | URL | |
BibTeX:
@book{akay_biomedical_2012,
author = {Akay, Metin},
title = {Biomedical signal processing},
publisher = {Elsevier Science},
year = {2012},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwY2AwNtIz0EUrE4D1tqVxoqllomEysL5PS05KNUoDVjXAxkVakqk5eIgXaWQbW78RZQM6bATDBDQJZ2rGzMAM7OQh5cpM0Oge6EYJQ0PwDC3QHhNQXwB64g6Mb4By-B64RnETZGBNBW0zEGJgSs0TZuBGOhZQmIHDFzrhLcIg4wTeHg8KSQXQUgsgVQBZ2g9UKcog6-Ya4uyhCzI9HjoQE58Eda6BsRgDbyJoAXteCXijW4oEg4KhUUqaeRpQhZlRqolRUmpSYqpFKvhiqeTEVGNDQ0kGMeyGSeGSkGbgAtbuRpDxAhkGlpKi0lRZiIcBZpdvhQ}
}
|
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| Millikan, R.G. | Biosemantics [BibTeX] |
1989 | The Journal of Philosophy Vol. 86(6), pp. 281-297 |
article | |
BibTeX:
@article{millikan_biosemantics_1989,
author = {Millikan, Ruth G.},
title = {Biosemantics},
journal = {The Journal of Philosophy},
year = {1989},
volume = {86},
number = {6},
pages = {281--297}
}
|
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| Millikan, R.G. | Biosemantics | 2009 | Vol. 1, pp. 394-407 |
incollection | URL |
| Abstract: Introduction – Mental Causation – The Causal Closure of the Physical and Naturalism – Dualism – Epiphenomenalism – Anomalous Monism – Non-reductive Materialism – Functionalism – What is Property Physicalism? – What is the Physical? – Idealism – Panpsychism – Subjectivity – Higher-order Theories of Consciousness – Representationalist Theories of Consciousness – Sensory Qualities, Sensible Qualities, Sensational Qualities – The Explanatory Gap – Phenomenal Concepts – The Two-dimensional Argument Against Materialism – Intentional Systems Theory – Wide Content – Narrow Content – Information-theoretic Semantics – Biosemantics – A Measurement-theoretic Account of Propositional Attitudes – The Normativity of the Intentional – Concepts and Possession Conditions – The Distinction Between Conceptual and Nonconceptual Content – Intentionalism – The Content of Perceptual Experience – Phenomenology, Intentionality, and the Unity of the Mind – The Self – Unity of Consciousness – Personal Identity and Metaphysics – Imagination – Thinking – Language and Thought – Consciousness and Reference – Memory – Emotions: Motivating Feelings – Intention and Intentional Action – Folk Psychology – Other Minds – Introspection – Semantic Externalism and Self-knowledge – Self-Deception; The term ‘biosemantics’ has usually been applied only to the theory of mental representation. This article first characterizes a more general class of theories called ‘teleological theories of mental content’ of which biosemantics is an example. Then it discusses the details that distinguish biosemantics from other naturalistic teleological theories. Naturalistic theories of mental representation attempt to explain, in terms designed to fit within the natural sciences, what it is about a mental representation that makes it represent something. Frequently these theories have been classified as either picture theories, causal or covariation theories, information theories, functionalist or causal-role theories, or teleological theories, the assumption being that these various categories are side by side with one another. | |||||
BibTeX:
@incollection{millikan_biosemantics_2009,
author = {Millikan, Ruth G.},
title = {Biosemantics},
publisher = {Oxford University Press},
year = {2009},
volume = {1},
pages = {394--407},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwzV1LT8MwDI4QSBOCA-NRxkPiAkigdk3Spe2BC-MxiXFiSNyitkm1gbYKtv1_7KZdt4FA3Lg1VZpYduTY7mebEM4c117SCX6QeDSOQV0mWI2Fi0iIlg4DHbXiJFFqKbJddvir3v1zwS9ZxDg8ZW4Vfp0JvkgD7EQjhZNyoFvZsyD_pf44GKkZrzHk8lb8D5pO-pf3Br47f5quB9lYD0EKJTi-DBQgDMo2qZI_JSAu-JMuglHBxSlUotFp3HQhLq5HzzSp_aJ5TVWqLN-kHxvcRbWc4-aVZJlXXTszMODCRGyLidmwLUkl87sSNpf0DMugD9UgmVzpkf38BDcupQIBfGVloFfj67RgIVM3ySwnihJLs-Vr5LwgtlmS2vyeUJPwOGdr9LbIBuafnGBiCNBfJyt6tE3WK_HtwIQ5aeyS3t1tr92xi64WdhaE1BYBhgEYGLqcqYSCuagD8AG1H9NAp1SwCAx2cMtdzXnMlQJ31lOREvCUpoxRvkc2I0x-wD1A1MoiaykcWG2h9WABrRapvYTdm6Dz0DbDejl0xnkmn_M-scBYyc-7LRx_n5wkXhR6IbY68D0vAldGh4LGqaJcMaHDsEGawA2Z9TNpUAtclvyTi_ID_knkX4Nc5F-MM_m7gA_-MvmQrFfH-4isTj6m-thU0fwECXxJzQ}
}
|
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| Barbieri, M. | Biosemiotics: a new understanding of life | 2008 | Naturwissenschaften Vol. 95(7), pp. 577-599 |
article | |
| Abstract: Biosemiotics is the idea that life is based on semiosis, i.e., on signs and codes. This idea has been strongly suggested by the discovery of the genetic code, but so far it has made little impact in the scientific world and is largely regarded as a philosophy rather than a science. The main reason for this is that modern biology assumes that signs and meanings do not exist at the molecular level, and that the genetic code was not followed by any other organic code for almost four billion years, which implies that it was an utterly isolated exception in the history of life. These ideas have effectively ruled out the existence of semiosis in the organic world, and yet there are experimental facts against all of them. If we look at the evidence of life without the preconditions of the present paradigm, we discover that semiosis is there, in every single cell, and that it has been there since the very beginning. This is what biosemiotics is really about. It is not a philosophy. It is a new scientific paradigm that is rigorously based on experimental facts. Biosemiotics claims that the genetic code (1) is a real code and (2) has been the first of a long series of organic codes that have shaped the history of life on our planet. The reality of the genetic code and the existence of other organic codes imply that life is based on two fundamental processes–copying and coding–and this in turn implies that evolution took place by two distinct mechanisms, i.e., by natural selection (based on copying) and by natural conventions (based on coding). It also implies that the copying of genes works on individual molecules, whereas the coding of proteins operates on collections of molecules, which means that different mechanisms of evolution exist at different levels of organization. This review intends to underline the scientific nature of biosemiotics, and to this purpose, it aims to prove (1) that the cell is a real semiotic system, (2) that the genetic code is a real code, (3) that evolution took place by natural selection and by natural conventions, and (4) that it was natural conventions, i.e., organic codes, that gave origin to the great novelties of macroevolution. Biological semiosis, in other words, is a scientific reality because the codes of life are experimental realities. The time has come, therefore, to acknowledge this fact of life, even if that means abandoning the present theoretical framework in favor of a more general one where biology and semiotics finally come together and become biosemiotics.;Biosemiotics is the idea that life is based on semiosis, i.e., on signs and codes. This idea has been strongly suggested by the discovery of the genetic code, but so far it has made little impact in the scientific world and is largely regarded as a philosophy rather than a science. The main reason for this is that modern biology assumes that signs and meanings do not exist at the molecular level, and that the genetic code was not followed by any other organic code for almost four billion years, which implies that it was an utterly isolated exception in the history of life. These ideas have effectively ruled out the existence of semiosis in the organic world, and yet there are experimental facts against all of them. If we look at the evidence of life without the preconditions of the present paradigm, we discover that semiosis is there, in every single cell, and that it has been there since the very beginning. This is what biosemiotics is really about. It is not a philosophy. It is a new scientific paradigm that is rigorously based on experimental facts. Biosemiotics claims that the genetic code (1) is a real code and (2) has been the first of a long series of organic codes that have shaped the history of life on our planet. The reality of the genetic code and the existence of other organic codes imply that life is based on two fundamental processes—copying and coding—and this in turn implies that evolution took place by two distinct mechanisms, i.e., by natural selection (based on copying) and by natural conventions (based on coding). It also implies that the copying of genes works on individual molecules, whereas the coding of proteins operates on collections of molecules, which means that different mechanisms of evolution exist at different levels of organization. This review intends to underline the scientific nature of biosemiotics, and to this purpose, it aims to prove (1) that the cell is a real semiotic system, (2) that the genetic code is a real code, (3) that evolution took place by natural selection and by natural conventions, and (4) that it was natural conventions, i.e., organic codes, that gave origin to the great novelties of macroevolution. Biological semiosis, in other words, is a scientific reality because the codes of life are experimental realities. The time has come, therefore, to acknowledge this fact of life, even if that means abandoning the present theoretical framework in favor of a more general one where biology and semiotics finally come together and become biosemiotics.;Biosemiotics is the idea that life is based on semiosis, i.e., on signs and codes. This idea has been strongly suggested by the discovery of the genetic code, but so far it has made little impact in the scientific world and is largely regarded as a philosophy rather than a science. The main reason for this is that modern biology assumes that signs and meanings do not exist at the molecular level, and that the genetic code was not followed by any other organic code for almost four billion years, which implies that it was an utterly isolated exception in the history of life. These ideas have effectively ruled out the existence of semiosis in the organic world, and yet there are experimental facts against all of them. If we look at the evidence of life without the preconditions of the present paradigm, we discover that semiosis is there, in every single cell, and that it has been there since the very beginning. This is what biosemiotics is really about. It is not a philosophy. It is a new scientific paradigm that is rigorously based on experimental facts. Biosemiotics claims that the genetic code (1) is a real code and (2) has been the first of a long series of organic codes that have shaped the history of life on our planet. The reality of the genetic code and the existence of other organic codes imply that life is based on two fundamental processes–copying and coding–and this in turn implies that evolution took place by two distinct mechanisms, i.e., by natural selection (based on copying) and by natural conventions (based on coding). It also implies that the copying of genes works on individual molecules, whereas the coding of proteins operates on collections of molecules, which means that different mechanisms of evolution exist at different levels of organization. This review intends to underline the scientific nature of biosemiotics, and to this purpose, it aims to prove (1) that the cell is a real semiotic system, (2) that the genetic code is a real code, (3) that evolution took place by natural selection and by natural conventions, and (4) that it was natural conventions, i.e., organic codes, that gave origin to the great novelties of macroevolution. Biological semiosis, in other words, is a scientific reality because the codes of life are experimental realities. The time has come, therefore, to acknowledge this fact of life, even if that means abandoning the present theoretical framework in favor of a more general one where biology and semiotics finally come together and become biosemiotics.; | |||||
BibTeX:
@article{barbieri_biosemiotics:_2008,
author = {Barbieri, Marcello},
title = {Biosemiotics: a new understanding of life},
journal = {Naturwissenschaften},
year = {2008},
volume = {95},
number = {7},
pages = {577--599}
}
|
|||||
| Biro, J.C. | Coding nucleic acids are chaperons for protein folding: A novel theory of protein folding | 2013 | Gene Vol. 515(2), pp. 249-257 |
article | URL |
| Abstract: The arguments for nucleic acid chaperons are reviewed and three new lines of evidence are added. (1) It was found that amino acids encoded by codons in short nucleic acid loops frequently form turns and helices in the corresponding protein structures. (2) The amino acids encoded by partially complementary (1st and 3rd nucleotides) codons are more frequently co-located in the encoded proteins than expected by chance. (3) There are significant correlations between thermodynamic changes (ddG) caused by codon mutations in nucleic acids and the thermodynamic changes caused by the corresponding amino acid mutations in the encoded proteins. We conclude that the concept of the Proteomic Code and nucleic acid chaperons seems correct from the bioinformatics point of view, and we expect to see direct biochemical experiments and evidence in the near future. © 2012 Elsevier B.V.; The arguments for nucleic acid chaperons are reviewed and three new lines of evidence are added. (1) It was found that amino acids encoded by codons in short nucleic acid loops frequently form turns and helices in the corresponding protein structures. (2) The amino acids encoded by partially complementary (1st and 3rd nucleotides) codons are more frequently co-located in the encoded proteins than expected by chance. (3) There are significant correlations between thermodynamic changes (ddG) caused by codon mutations in nucleic acids and the thermodynamic changes caused by the corresponding amino acid mutations in the encoded proteins. We conclude that the concept of the Proteomic Code and nucleic acid chaperons seems correct from the bioinformatics point of view, and we expect to see direct biochemical experiments and evidence in the near future.; The arguments for nucleic acid chaperons are reviewed and three new lines of evidence are added. (1) It was found that amino acids encoded by codons in short nucleic acid loops frequently form turns and helices in the corresponding protein structures. (2) The amino acids encoded by partially complementary (1st and 3rd nucleotides) codons are more frequently co-located in the encoded proteins than expected by chance. (3) There are significant correlations between thermodynamic changes (ddG) caused by codon mutations in nucleic acids and the thermodynamic changes caused by the corresponding amino acid mutations in the encoded proteins. We conclude that the concept of the Proteomic Code and nucleic acid chaperons seems correct from the bioinformatics point of view, and we expect to see direct biochemical experiments and evidence in the near future. | |||||
BibTeX:
@article{biro_coding_2013,
author = {Biro, Jan C.},
title = {Coding nucleic acids are chaperons for protein folding: A novel theory of protein folding},
journal = {Gene},
year = {2013},
volume = {515},
number = {2},
pages = {249--257},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV3db9MwED8hvjSEgH0QyofkF3iBVElsJy5vXUc1iT0OCZ4sx461Tls6mmza_nvunKbdCkgg5cGWLcvxnX13vt-dAXg2TOKNM4GbMleGc0_puBzKPDwdS-GcN1lRycLfvdmGT39x6AdgFi4s5bdMs3CPJyjQVwhOcK7pwf76FJay8yCQlZSmo2XAzJ-HuCOUlkfzSiA9pPiQy-aW2Jk-hx5138NNVj7odZT873Dsf_qdF_BsqYuyccc823Cvqndgd1yjHX5-wz6wgA4N1-478Gi_Lz25lcJwF35M5iT9WE15kWeWGTtzDTOLitkTQ0nI64ahXsxCPohZjeXg7frMxqyeX1VnLERS3rC53-yyB9-mX44nh_HyuYbY8oKLWEhfGe5RH0iULaxIfaa846kxLimTEg095SySvDAjL3InUHGphJJkwhlvSs9fwlNDsP66DeF_LoIHHvdgFZFcjHDpI3j8fXR0oA6_Trrqdl8dNiFGbfizjZABwhaO82HxCljmvZMyNyMlrci5xcmI0qbKCZdnqfED-NiTXl90CT50j3w71UQcTcTR-CFxBhARd2ja_e3CWM1TWXC0uRJs6RhmNQrqqmgbCjmA9x0HrVt0g6NphcYiLgoadFK31y2OsNFPZqi9Fkq8_q85voGtLLzZQZibt3C_XVxW77osk78AAC4Hcw}
}
|
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| Millikan, R.G. | Compare and Contrast Dreske, Fodor, and Millikan on Teleosemantics [BibTeX] |
1990 | Philosophical Topics Vol. 18(2), pp. 151 |
article | URL |
BibTeX:
@article{millikan_compare_1990,
author = {Millikan, Ruth G.},
title = {Compare and Contrast Dreske, Fodor, and Millikan on Teleosemantics},
journal = {Philosophical Topics},
year = {1990},
volume = {18},
number = {2},
pages = {151},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw3V3JTsMwELVYJFQJIcoSdvnEJU2UjTQ5cKAtpRIckAhSb5VjO6KiTaFN_5-xHSctyw9wyMF2lEzmWZ4ZZ_wGId-zHevbmuDzLKRuzJ1U8I-5hAmaNc5vsrCdeXFG1ne2qwKodd9_AL6rssrlXwHBPTUni8LsQVSt0nD6EIdWOZviJOD4XVSnyM0EDNBswaegap0BXzqtz7rcgQQ0mX2sZMjrJ0iolsWb-aByf-vdBBcsUZWXVu4mirp9JUeDueISVy9aXZ-8dgi6VoWYbC77wIEILLiGvy-wVZyrVkvwNq4Fw_mUjWlxy3Pr9WUTwudIEh07HW1RRVApacD0C3_YTekMJPtorxQZ3yntN9EGzw9Qoxb_EHVKGDCoGWsYsIKhhSUILTmmFYhnOV6H4Ahd9e-T7sDSUozYZDICzykQbPZx5B-jXSIOKIi7QdPMQNsZTCpuCAtvgLgG2hnGT71o8NhVzaZu2gt52s7-LAz4fDknrdBunyDMXM-jjILDlZIg9UnsuTRgaUbiiIYRdU6R8Yc8Z3-OnKNGPQsu0FYxX_JLxUj5BbWYL4M}
}
|
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| Chaitin, G.J. | Computers, paradoxes and the foundations of mathematics | 2002 | American Scientist [H.W. Wilson - GS] Vol. 90(2), pp. 164 |
article | URL |
| Abstract: The consideration of the inherent paradoxes and randomness in mathematics by some of the great thinkers of the 20th century has benefited computer science. At the start of the 20th century, the well-known German mathematician David Hilbert proposed formalizing completely all of mathematical reasoning.Hilbert's proposal was driven by the logical paradoxes that his contemporary Bertrand Russell had highlighted; that is, cases where reasoning that seems to be sound leads to contradictions. However, Kurt Godel and Alan Turing showed that mathematical reasoning cannot be formalized. Their work was taken a step further by the author whose research demonstrates that randomness is natural and inevitable in mathematics. Nevertheless, formalism has been one of the biggest boons of the 20th century for programming, for calculating, and for computing. | |||||
BibTeX:
@article{chaitin_computers_2002,
author = {Chaitin, Gregory J.},
title = {Computers, paradoxes and the foundations of mathematics},
journal = {American Scientist [H.W. Wilson - GS]},
year = {2002},
volume = {90},
number = {2},
pages = {164},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1NTwMhEJ1ovXhRW238asJRE9esLGXhZNTY-AM8eGuAZU51V11N_PkFChitXjxDCAkwvGEe7wFU9LIsfsSEqUNH2jgowmuma0TjkKyWdIqcUhRovr9sQ1KFiKudgmSI3E1n_KO5z9qFu2uEuH55LbyLlK-2RkuNTdhyuCEc1PrpNlcVfMkoO-hJydfib7hUZruQWE6JTJIrzF9_4NfJ1v-d7B7sRPBJbla7ZQgbth153-bI8RjBMB71npxFPerzfaiT80N_QbxSeNN9ug6qbYgDjwSzL1NPOiTPWQa2P4DJ7P7x7qFIc503i8XcZ4JMsqqqxjBou9YeAlFMXFlaMlsqwwSTiiMqiUK7rIVbqo9g_PsYx381nMB2MFQJNK5TGLy_fdjJSgNxCbsTqcQ}
}
|
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| Shea, N. | Consumers Need Information: Supplementing Teleosemantics with an Input Condition | 2007 | Philosophy and Phenomenological Research Vol. 75(2), pp. 404-435 |
article | URL |
| Abstract: The success of a piece of behaviour is often explained by its being caused by a true representation (similarly, failure falsity). In some simple organisms, success is just survival and reproduction. Scientists explain why a piece of behaviour helped the organism to survive and reproduce by adverting to the behaviour's having been caused by a true representation. That usage should, if possible, be vindicated by an adequate naturalistic theory of content. Teleosemantics cannot do so, when it is applied to simple representing systems (Godfrey-Smith 1996). Here it is argued that the teleosemantic approach to content should therefore be modified, not abandoned, at least for simple representing systems. The new 'infotel-semantics' adds an input condition to the output condition offered by teleosemantics, recognising that it is constitutive of content in a simple representing system that the tokening of a representation should correlate probabilistically with the obtaining of its specific evolutionary success condition.; The success of a piece of behaviour is often explained by its being caused by a true representation (similarly, failure falsity). In some simple organisms, success is just survival and reproduction. Scientists explain why a piece of behaviour helped the organism to survive and reproduce by adverting to the behaviour’s having been caused by a true representation. That usage should, if possible, be vindicated by an adequate naturalistic theory of content. Teleosemantics cannot do so, when it is applied to simple representing systems (Godfrey‐Smith 1996). Here it is argued that the teleosemantic approach to content should therefore be modified, not abandoned, at least for simple representing systems. The new ‘infotel‐semantics’ adds an input condition to the output condition offered by teleosemantics, recognising that it is constitutive of content in a simple representing system that the tokening of a representation should correlate probabilistically with the obtaining of its specific evolutionary success condition.; The success of a piece of behaviour is often explained by its being caused by a true representation (similarly, failure falsity). In some simple organisms, success is just survival and reproduction. Scientists explain why a piece of behaviour helped the organism to survive and reproduce by adverting to the behaviour's having been caused by a true representation. That usage should, if possible, be vindicated by an adequate naturalistic theory of content. Teleosemantics cannot do so, when it is applied to simple representing systems (Godfrey-Smith 1996). Here it is argued that the teleosemantic approach to content should therefore be modified, not abandoned, at least for simple representing systems. The new 'infotel-semantics' adds an input condition to the output condition offered by teleosemantics, recognising that it is constitutive of content in a simple representing system that the tokening of a representation should correlate probabilistically with the obtaining of its specific evolutionary success condition. | |||||
BibTeX:
@article{shea_consumers_2007,
author = {Shea, Nicholas},
title = {Consumers Need Information: Supplementing Teleosemantics with an Input Condition},
journal = {Philosophy and Phenomenological Research},
year = {2007},
volume = {75},
number = {2},
pages = {404--435},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1La9tAEB5KAsUQ2qZNVPUBe-hV7j70WOUSgttgaCmmpNCbWO2uIJCkTqRA–87s3rUDgmkNwvb8lozu983s7PfACg558mdNQEtTdJQhtvUpbKR0nCnLS9rX0qdebud2Z4yGVRkGaoEw54-0qX6wn8kr8MZmh2vrxPqHkW7rEMrDVyKBTKSXid3WpALLgZ1RpEg4GVbEDQsxH0x4h302SasAXFOn8NY4jZWmkzbz_8OyN9Tif2f_-QFPBsYKTvpXWgfnvirlzBbjS0O_ryC1WI4p9mybwh2bDjCRCY9YqEtaMgxIgiyM0SxX62_RHud25ZRlpeZK_zG-rZjeBsXKsQO4Mfp57PFMhk6MSQWI0CMVptCKVU3RFAwBKqRJDiufZo3RuomS63mGfdlKb0WaVHkVjjts9zItFbOaq0OYc9QxT79OHJoF8Fug9PLRwR5ET7aCJ7-LL9-0ssvi_5yf7yct-H42fy6i9Cg4eEk-bx4DQy9JzeFk6FZiBWpaZTzJOYjiMakJgYx2rla99od1UbMUypVIZmT1IkzbMJrWf2OISKHqGh6dzfGVqIQiO6iLGM4DAacbjVaL4YPm04zvc97fTgMSAMxx9E85mOLQZqdJAm6GPLggI8efrVarr7jqzcPDfYtzPrsNFXJvYOd7ubWv-8lKP8CBMYWLQ}
}
|
|||||
| Wurm, M.F. and Lingnau, A. | Decoding actions at different levels of abstraction | 2015 | The Journal of neuroscience : the official journal of the Society for Neuroscience Vol. 35(20), pp. 7727 |
article | URL |
| Abstract: Brain regions that mediate action understanding must contain representations that are action specific and at the same time tolerate a wide range of perceptual variance. Whereas progress has been made in understanding such generalization mechanisms in the object domain, the neural mechanisms to conceptualize actions remain unknown. In particular, there is ongoing dissent between motor-centric and cognitive accounts whether premotor cortex or brain regions in closer relation to perceptual systems, i.e., lateral occipitotemporal cortex, contain neural populations with such mapping properties. To date, it is unclear to which degree action-specific representations in these brain regions generalize from concrete action instantiations to abstract action concepts. However, such information would be crucial to differentiate between motor and cognitive theories. Using ROI-based and searchlight-based fMRI multivoxel pattern decoding, we sought brain regions in human cortex that manage the balancing act between specificity and generality. We investigated a concrete level that distinguishes actions based on perceptual features (e.g., opening vs closing a specific bottle), an intermediate level that generalizes across movement kinematics and specific objects involved in the action (e.g., opening different bottles with cork or screw cap), and an abstract level that additionally generalizes across object category (e.g., opening bottles or boxes). We demonstrate that the inferior parietal and occipitotemporal cortex code actions at abstract levels whereas the premotor cortex codes actions at the concrete level only. Hence, occipitotemporal, but not premotor, regions fulfill the necessary criteria for action understanding. This result is compatible with cognitive theories but strongly undermines motor theories of action understanding. | |||||
BibTeX:
@article{wurm_decoding_2015,
author = {Wurm, Moritz F. and Lingnau, Angelika},
title = {Decoding actions at different levels of abstraction},
journal = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
year = {2015},
volume = {35},
number = {20},
pages = {7727},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw3V27TsMwFLWgEwsCyhskTyxVUGLHeQwMFQ-VhQHKXF07TlWgSVXSAb4eO3YSt4IfYLXjIT7Wsc-918cIUXLtexucoEiP-sBTEDSJOFOcKCkQwmUsY4AUNiLbzTuAXdt_AP5OCcr6poq5svCprys2z6BUgw9dJFSXbwDXUQ7RAvPWrRvnlOr4XcpBUwTym–EbndLQJ-cgS3zr5YmAlsuZ9V3V1SsBPG0gJUpsJzKj9k7uNGIgOlEOjGJFWkZlNQpm8ClWONIYpeS_dwQpjrcx2tMvpgrLIi2QQstTa_bYbdd2hp9ns1EdSML7_VlW-nuRKvv59FjuxXHim-03bMdsyEd6iPEeA_t2lnFQ4PZPtqSxQHqDwuoyvkXvsJ1NW6d5ugj2sCILYwYKtzCiA2MuMyxA-MhGj_cj29Hnn3gwlskNPaygMRBQLkfUh5QIbnghFEZ5kz6uQSuNqqIQCYZy5XsYzwWUZaRPEkhVP0R0CPUK8pCniDMqYggCjjTAp8mSUoy7VSXpSIkoYD0FB2bP58sjInJpJmTsz97ztFOh_AF6lXLlbw0bpU_dbg5-A}
}
|
|||||
| Griffiths, P.E. and Gray, R.D. | Developmental Systems and Evolutionary Explanation [BibTeX] |
1994 | The Journal of Philosophy Vol. 91(6), pp. 277-304 |
article | URL |
BibTeX:
@article{griffiths_developmental_1994,
author = {Griffiths, P. E. and Gray, R. D.},
title = {Developmental Systems and Evolutionary Explanation},
journal = {The Journal of Philosophy},
year = {1994},
volume = {91},
number = {6},
pages = {277--304},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV3fS8MwED5EQQaiTl2tOuiDr61r-jNPInNjoMgeFPZW0iT1ZYxtVsH_3ru03aYM1MdCKEkuufsu-fIdQMC8nvvDJ0RCC-4XRSyTgMmUY5xKYgTPLAhYIEzVzo2TbWiKOhLJ0rAEzZ0-wqV8qm8Yx5wkZbfzhUvFo-iSta6kgZ7YR0BSyeSu_XHUED2Yi-56snK-FQHxG7TcEnxMoBkeQcMFaAgmq1vn9bv4LQTs_w3gGA5rHOrcVQunDTt6dgKtcVPY4PMU2AafCFvW0uaOmCln8FEvWOyZQyw-UZ0pnsHLcPDcH7l1hQX3FcO-7_q-VCzWBZlGFpjaxEkgBUIKnocCt4-OU1GEKkFcolPJBWc651S2Ks9ZxHgadOBAEBN_VpoXe8qCvQK3jbYolFk4dxbsT_jjfTp66Fef7ebTezPPyrxFaaGlzPDd2EvOwUkINqCnCGVQhH5PiyTKVS9VBc_9XGllQ4cMmNEWLJdCZpiD8hi7ZUPXTHY2r5Q6MsxwiOie1TNug9WYOlPTaUZncAkVAe7ZcL1p-dUPSBQ4fBqTKB6hYRv8vzTr1_LqJCtQXvzSqUtoVfrMdLJzBbvl8l13K1HIL9Ib9b0}
}
|
|||||
| Griffiths, P.E. and Gray, R.D. | Discussion: Three Ways to Misunderstand Developmental Systems Theory | 2005 | Biology & Philosophy Vol. 20(2), pp. 417-425 |
article | URL |
| Abstract: Developmental systems theory (DST) is a general theoretical perspective on development, heredity and evolution. It is intended to facilitate the study of interactions between the many factors that influence development without reviving `dichotomous' debates over nature or nurture, gene or environment, biology or culture. Several recent papers have addressed the relationship between DST and the thriving new discipline of evolutionary developmental biology (EDB). The contributions to this literature by evolutionary developmental biologists contain three important misunderstandings of DST.; Developmental systems theory (DST) is a general theoretical perspective on development, heredity and evolution. It is intended to facilitate the study of interactions between the many factors that influence development without reviving `dichotomous' debates over nature or nurture, gene or environment, biology or culture. Several recent papers have addressed the relationship between DST and the thriving new discipline of evolutionary developmental biology (EDB). The contributions to this literature by evolutionary developmental biologists contain three important misunderstandings of DST.[PUBLICATION ABSTRACT]; Developmental systems theory (DST) is a general theoretical perspective on development, heredity and evolution. It is intended to facilitate the study of interactions between the many factors that influence development without reviving `dichotomous' debates over nature or nurture, gene or environment, biology or culture. Several recent papers have addressed the relationship between DST and the thriving new discipline of evolutionary developmental biology (EDB). The contributions to this literature by evolutionary developmental biologists contain three important misunderstandings of DST. | |||||
BibTeX:
@article{griffiths_discussion:_2005,
author = {Griffiths, Paul E. and Gray, Russell D.},
title = {Discussion: Three Ways to Misunderstand Developmental Systems Theory},
journal = {Biology & Philosophy},
year = {2005},
volume = {20},
number = {2},
pages = {417--425},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV3fS90wFD6IwyGM-WOuu1OhD9vLoKVN2qbZ27hXEVSQzf14C2mTgih3uvbC7n-_k6Tp7dQHfSwNp2lyes6X5nxfACiJk-heTKjzktaInmWNmL-RVZpwIllRcEV0qiyte_RnG8jwJ2N-HfsNShu3R9S3nPLIllEg5I3MAghTlfHxr99-DLHYZHun7s0jWhbM72s-ZuH_zDSCm4YfsmhHW6WPJimbkI63wBNlfCHKsDu94s8_LNR-xotuw-seq4ZfnHPtwJqe78KGO71yuQubF_4YhOUbmM2u2nphSmrnn8NLdBAd_pTLNux-h-dXhgXYU2jCUZUS2u4F00MnEbAH34-PLqcnUX9CQ1Sb46kj1XCdMFVpRBWkobqq0oorpmlVN5JjMMmaysjxqEwpiT4g0xRnnCAuYIzShtG38EqaSv55Zxl_KoAXDX52OjCpMMAxDeDlL342K09Op-5yx1_GraWlxXddgLNtv9qoiNk7CHWOj1IFgiNcXFJeV5LlhUyIqjkupvJmAp_8RItbp-khVurNZrgFDrcwwy3SCQTeFYS6uRGIeEqKq8oE73x0njEYIaIlIhGU4pMzWuS8FN3fDi3ca5dlCNNyxifwwc_5ygaGReE6QRK0iJ3AZmN3G5pasSJqIJhF8hNIn9Js2mu_G82D7v3TerAPm1ay1tbeHcB692ehD51w5T-gjx-d}
}
|
|||||
| Shamir, M. | Emerging principles of population coding: in search for the neural code | 2014 | Current Opinion in Neurobiology Vol. 25, pp. 140 - 148 |
article | DOI URL |
| Abstract: Population coding theory aims to provide quantitative tests for hypotheses concerning the neural code. Over the last two decades theory has focused on analyzing the ways in which various parameters that characterize neuronal responses to external stimuli affect the information content of these responses. This article reviews and provides an intuitive explanation for the major effects of noise correlations and neuronal heterogeneity, and discusses their implications for our ability to investigate the neural code. It is argued that to test neural code hypotheses further, additional constraints are required, including relating trial-to-trial variation in neuronal population responses to behavioral decisions and specifying how information is decoded by downstream networks. | |||||
BibTeX:
@article{shamir_emerging_2014,
author = {Shamir, Maoz},
title = {Emerging principles of population coding: in search for the neural code},
journal = {Current Opinion in Neurobiology},
year = {2014},
volume = {25},
pages = {140 -- 148},
url = {http://www.sciencedirect.com/science/article/pii/S0959438814000105},
doi = {http://doi.org/10.1016/j.conb.2014.01.002}
}
|
|||||
| Collier, J. | Explaining biological functionality : is control theory enough? | 2011 | South African Journal of Philosophy = Suid-Afrikaanse Tydskrif vir Wysbegeerte Vol. 30(1), pp. 53-62 |
article | |
| Abstract: It is generally agreed that organisms are Complex Adaptive Systems. Since the rise of Cybernetics in the middle of the last century ideas from information theory and control theory have been applied to the adaptations of biological organisms in order to explain how they work. This does not, however, explain functionality, which is widely but not universally attributed to biological systems. There are two approaches to functionality, one based on etiology (what a trait was selected for), and the other based in autonomy. I argue that the etiological approach, as understood in terms of control theory, suffers from a problem of symmetry, by which function can equally well be placed in the environment as in the organism. Focusing on the autonomy view, I note that it can be understood to some degree in terms of control theory in its version called second order cybernetics. I present an approach to second order cybernetics that seems plausible for organisms with limited computational power, due to Hooker, Penfold and Evans. They hold that this approach gives something like concepts, certainly abstractions from specific situations, a trait required for functionality in its system adaptive form (i.e., control of the system by itself). Using this cue, I argue that biosemiotics provides the methodology to incorporate these quasi concepts into an account of functionality.;It is generally agreed that organisms are Complex Adaptive Systems. Since the rise of Cybernetics in the middle of the last century ideas from information theory and control theory have been applied to the adaptations of biological organisms in order to explain how they work. This does not, however, explain functionality, which is widely but not universally attributed to biological systems. There are two approaches to functionality, one based on etiology (what a trait was selected for), and the other based in autonomy. I argue that the etiological approach, as understood in terms of control theory, suffers from a problem of symmetry, by which function can equally well be placed in the environment as in the organism. Focusing on the autonomy view, I note that it can be understood to some degree in terms of control theory in its version called second order cybernetics. I present an approach to second order cybernetics that seems plausible for organisms with limited computational power, due to Hooker, Penfold and Evans. They hold that this approach gives something like concepts, certainly abstractions from specific situations, a trait required for functionality in its system adaptive form (i.e., control of the system by itself). Using this cue, I argue that biosemiotics provides the methodology to incorporate these quasi concepts into an account of functionality. [PUBLICATION ABSTRACT]; | |||||
BibTeX:
@article{collier_explaining_2011,
author = {Collier, John},
title = {Explaining biological functionality : is control theory enough?},
journal = {South African Journal of Philosophy = Suid-Afrikaanse Tydskrif vir Wysbegeerte},
year = {2011},
volume = {30},
number = {1},
pages = {53--62}
}
|
|||||
| Frieden, B.R., Plastino, A. and Plastino, A.R. | Fisher order measure and Petri’s universe [BibTeX] |
2011 | Physica A: Statistical Mechanics and its Applications | article | URL |
BibTeX:
@article{frieden_fisher_2011,
author = {Frieden, B. R. and Plastino, A. and Plastino, A. R.},
title = {Fisher order measure and Petri’s universe},
journal = {Physica A: Statistical Mechanics and its Applications},
year = {2011},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwY2AwNtIz0EUrE1LNkpOSTNOMUpLTktPMTVKSLdOAFV-KmVFiiqm5cbI56sg2Yu862oQ-eGEWqMufCDl8E3T-JrjvY2JiDFrP5ebiBC-GDc2NIVMIwG6SibG5IezIIexmIFVLSPWLmwADbHMDbF0JfLIZsR0ec901ce4WZOCHtjoVHCHJRIiBKTVPmIEdvPozuViEQRtyAboC-BxOhVzIsKFCYl6KAvjCrUcNM4sVSiErOFJFGYzdXEOcPXRhHokvgBxYEQ9byZUVD3ZDPMgNwKZ_PKguF2PgTQStpc8rAe-5S5FgUEhJszBKszC3SEwyTDIxT0lMSrYwTDNPAsYdMI8mGxtJMuiQYoUUacqlGbjA47bgJSMyDCwlRaWpspBDEgFEY619}
}
|
|||||
| Stegmann, U.E. | Genetic Information as Instructional Content [BibTeX] |
2005 | Philosophy of Science Vol. 72(3), pp. 425-443 |
article | |
BibTeX:
@article{stegmann_genetic_2005,
author = {Stegmann, Ulrich E},
title = {Genetic Information as Instructional Content},
journal = {Philosophy of Science},
year = {2005},
volume = {72},
number = {3},
pages = {425--443}
}
|
|||||
| Griffiths, P.E. | Genetic Information: A Metaphor in Search of a Theory [BibTeX] |
2001 | Philosophy of Science Vol. 68(3), pp. 394-412 |
article | |
BibTeX:
@article{griffiths_genetic_2001,
author = {Griffiths, Paul E.},
title = {Genetic Information: A Metaphor in Search of a Theory},
journal = {Philosophy of Science},
year = {2001},
volume = {68},
number = {3},
pages = {394--412}
}
|
|||||
| Graziano, M. | Genetics and Philosophy by Paul Griffiths and Karola Stotz: Cambridge: Cambridge University Press, 2013, pp. 270, £50 (hardback) [BibTeX] |
2015 | Australasian Journal of Philosophy Vol. 93(2), pp. 408-408 |
article | URL |
BibTeX:
@article{graziano_genetics_2015,
author = {Graziano, Mario},
title = {Genetics and Philosophy by Paul Griffiths and Karola Stotz: Cambridge: Cambridge University Press, 2013, pp. 270, £50 (hardback)},
journal = {Australasian Journal of Philosophy},
year = {2015},
volume = {93},
number = {2},
pages = {408--408},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3dS8MwED9EQQaizo9uOqH_QOuatGnrm0znYD4ITvCtJGnyuE3XPcy_3lyy7kNEYY-hbULvkrvL5Xe_AFASdoMfNkEg835OmWSl1onsCiI1E4xyQYQxiHw7sw01KwSCLHFHrR1thLXcuNS5mNX4uFtbFh3boqooDnPclVt6UJoiwmvUH6zLJDOXckHsRWaBPZ2_OtnyVFs8pkgrKifT-WzDFfVPoMZG1RCU1bn0unL-F4j2jr94CsfLkNW_d3OsCXtqfAaNl_oOhMU53CF5NfI9-2YIf_3EFwsfoYf-0zI15F4YIsiE-6_VpPq6gLf-46g3CJaXMgQSQwFjs6Xx8XkipSBUlSo3zk0oE5dpLjIWCcmUNmGdZprEOtKKM6LiLtUmLOFxzhS9hCOO4P1xZYv8Sg8OtFlpykPv5xlhenD4nj8_ZINhzzWbdTOc2Uq08KPyjE7tQg1YmLbAZ5pL5MlJSSljVbIskwkpSc6TtBtxmrchqHVZTB2NRxGt2FGddAuUbuGk24Z0U-FFZdMn2t118s-XLTc3VuNgSGnMZBJf7dzpNTRMK7GIIdqB_epzrm4cceQ3hiH1ag}
}
|
|||||
| Griffiths, P. and Stotz, K. | Genetics and philosophy: an introduction [BibTeX] |
2013 | book | URL | |
BibTeX:
@book{griffiths_genetics_2013,
author = {Griffiths, Paul and Stotz, Karola},
title = {Genetics and philosophy: an introduction},
publisher = {Cambridge University Press},
year = {2013},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwdZ07T8MwEIBPlAoUiYG21LwqZWJLyLN2RhqoKoEEAwNb5eeARMQjSM2_x3YeVQpssS6yLSvnc8533wHEkR94O3sCIXOqiEo5liqRqeA8pIxnXJ-2CWdE9j3b0KMVbKrtDe82B_03NXH39j_E1_ni0UL7wxDbysoDGJCe-r7WkVo4NXxAp3sxsDWFtDYYAHracHq6XhpSVCsnPYSftUvLYxhKk6wwgj1ZjGFyU-hf6LfKvXJtYKf1mI_hYNE-OU9t4YJqAsgQpw2k2aWFcN87yQnMlnfP-cozo60b986a6SNFqjVvE0_hiJqw-KK06XMCwVDpb1giY1eQnhmCw5fs4Zas7vO6OWqb_pfN8fI_SqTNmFUBb-7jU3AzrgQLRED1pp5gmTAWhIwGIlFJFKqYnMH07-mc_ye4ACeyNSWMH-MS9svPbzmrl_AHX2GYAw}
}
|
|||||
| Sarkar, S. | Genetics and reductionism [BibTeX] |
1998 | book | URL | |
BibTeX:
@book{sarkar_genetics_1998,
author = {Sarkar, Sahotra},
title = {Genetics and reductionism},
publisher = {Cambridge University Press},
year = {1998},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwdV09T8MwED1REKiCgRbqFqiUP5AojdvanluqSjAwMLBVTmxvRIJ2oP-eO9upUlS2nG7IObrcl_zeAfAiy9M_MUHzqlQzaUr0ATPTXBkszSttqyIXjnva7tZk-1TfeARAbyYYWD1gHy460MEmr_VXhjAsOdbOEZ865xQSDgK2ZirS7zTKaVtGvTxi5vPpZnUL5wRB6MGZrftw3dplsO_DZdgeiU_dt2YNwf4ORsQfTZTLia5N8k2ErH7Uuv28h_Hq-X2xTuk1mziu2ZTxUD_FAG40XXOvdx4OZxhcOPRJyyhPMDSJwdWHel3K9csiiL1GzLYes5V97RimJe_S6TwTQ0gEJiRlJs4ql0-trGh9pJ1UgpjbuBNyBIPT5jz8p3iEbgDq0VziKdo4Dh_vF5dlh8U}
}
|
|||||
| Chaitin, G.J. | Gödel's theorem and information [BibTeX] |
1982 | International Journal of Theoretical Physics Vol. 21(12), pp. 941-954 |
article | URL |
BibTeX:
@article{chaitin_gos_1982,
author = {Chaitin, Gregory J.},
title = {Gödel's theorem and information},
journal = {International Journal of Theoretical Physics},
year = {1982},
volume = {21},
number = {12},
pages = {941--954},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw3V07T8MwELagEhIL4imeUiQGplSO4yT2wAAVtDME1ip-RHRoQLT9a_wB_hh2fW5MsjCzRokl-6y773L3fYdQSoY47vgEoqistAmVdUrrtcyUzEWiKk0zlpjkrvNn288BbJ_9B8OPbe37Ple2_F4sgKk4B5WlDVcxBKX9v4IAUcuA5bhuFW0740dv1Qz0B4DmAgUm5Sh1jATdGL6jHxuU7RQvhxocYUFinrmpJt5TkiS8ESTwe9ypV0EI5U4Xuuedse85J5gZ4MDbGOTr7p3QtGkY9OLKwbdWGn2uZnJ5q5v45Xnb5N3MZt9Pk9dWdRlTF4phg7_1aWGlAJEE0KLcR3tw4NGds-UB2tLNIdqBAz9C0fj7y1jzZhGBLSNjyyiw5TEqHx_K0SSGwRaxNPlbrHlSU6mIFCyr6qLQShPOhHGushAGkDLKc4mFMr4_sVo8ibD8Z451lRe8Vio9QYPmvdGnKDJw0ZLmspxLQTM7m1GY1SlPGdUkFfkZuvZ7m344-ZJp_yzP__TWBdptb88lGiw_V_rKqVf-AM71Mkc}
}
|
|||||
| Schulte, P. | How Frogs See the World: Putting Millikan's Teleosemantics to the Test [BibTeX] |
2012 | Philosophia (United States) Vol. 40(3), pp. 483-496 |
article | |
BibTeX:
@article{schulte_how_2012,
author = {Schulte, Peter},
title = {How Frogs See the World: Putting Millikan's Teleosemantics to the Test},
journal = {Philosophia (United States)},
year = {2012},
volume = {40},
number = {3},
pages = {483--496}
}
|
|||||
| Bernhardt, H. and Tate, W. | Hypothesis The transition from noncoded to coded protein synthesis: did coding mRNAs arise from stability-enhancing binding partners to tRNA? | 2010 | BIOLOGY DIRECT Vol. 5 |
article | |
| Abstract: Background: Understanding the origin of protein synthesis has been notoriously difficult. We have taken as a starting premise Wolf and Koonin's view that "evolution of the translation system is envisaged to occur in a compartmentalized ensemble of replicating, co-selected RNA segments, i. e., in an RNA world containing ribozymes with versatile activities". Presentation of the hypothesis: We propose that coded protein synthesis arose from a noncoded process in an RNA world as a natural consequence of the accumulation of a range of early tRNAs and their serendipitous RNA binding partners. We propose that, initially, RNA molecules with 3' CCA termini that could be aminoacylated by ribozymes, together with an ancestral peptidyl transferase ribozyme, produced small peptides with random or repetitive sequences. Our concept is that the first tRNA arose in this context from the ligation of two RNA hairpins and could be similarly aminoacylated at its 3' end to become a substrate for peptidyl transfer catalyzed by the ancestral ribozyme. Within this RNA world we hypothesize that proto-mRNAs appeared first simply as serendipitous binding partners, forming complementary base pair interactions with the anticodon loops of tRNA pairs. Initially this may have enhanced stability of the paired tRNA molecules so they were held together in close proximity, better positioning the 3' CCA termini for peptidyl transfer and enhancing the rate of peptide synthesis. If there were a selective advantage for the ensemble through the peptide products synthesized, it would provide a natural pathway for the evolution of a coding system with the expansion of a cohort of different tRNAs and their binding partners. The whole process could have occurred quite unremarkably for such a profound acquisition. Testing the hypothesis: It should be possible to test the different parts of our model using the isolated contemporary 50S ribosomal subunit initially, and then with RNAs transcribed in vitro together with a minimal set of ribosomal proteins that are required today to support protein synthesis. Implications of the hypothesis: This model proposes that genetic coding arose de novo from complementary base pair interactions between tRNAs and single-stranded RNAs present in the immediate environment. Reviewers: This article was reviewed by Eugene Koonin, Rob Knight and Berthold Kastner (nominated by Laura Landweber). | |||||
BibTeX:
@article{bernhardt_hypothesis_2010,
author = {Bernhardt, HS and Tate, WP},
title = {Hypothesis The transition from noncoded to coded protein synthesis: did coding mRNAs arise from stability-enhancing binding partners to tRNA?},
journal = {BIOLOGY DIRECT},
year = {2010},
volume = {5}
}
|
|||||
| Godfrey-Smith, P. | Indication and Adaptation | 1992 | Synthese Vol. 92(2), pp. 283-312 |
article | URL |
| Abstract: This paper examines the relationship between a family of concepts involving reliable correlation, and a family of concepts involving adaptation and biological function, as these concepts are used in the naturalistic semantic theory of Dretske's "Explaining Behavior." I argue that Dretske's attempt to marry correlation and function to produce representation fails, though aspects of his failure point the way forward to a better theory. | |||||
BibTeX:
@article{godfrey-smith_indication_1992,
author = {Godfrey-Smith, Peter},
title = {Indication and Adaptation},
journal = {Synthese},
year = {1992},
volume = {92},
number = {2},
pages = {283--312},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV07T8MwED6hTl2AFgrhIUVigSGQxE5sT6ggKtgYYI5snz1VobwG_j12HIeKx8CcRIrO9r2-z98BkPI8z775BKzdmdKcipoalyFwVMIYLhSVSGzQ1V7rbA-dDE-y7FiCHabv0iW1NBc-ZLG8Ki9Xz5mfHuVR1n6UhnPFXqIsjDIfwARXEfTqjCJj3AeitRAUWIg_PHEXXhZbEPlskVYyYM1ft-F_oV3_87e3YbNPP9N52C8T2DDtFMb3cZ7BxxQm_Wl_TU97SeqzHUjuWuybe6lsMZ2jXAUMfxceFzcP17dZP1Qh066WqjKmmLFM20JZZBVaIpBpzS1SXUtiS8FlpfLC0JpqFAX1emZMaOkKC4raOYAZjNqn1uxD6p4iapNzxZHaQruCVBeEKmMqLK3UCZxEOzeroJ3RRJXkq4VX-qIkLxOYdbYaXomGSmAvrkmDy2VTeCyi4jXJD_765BDGgU7rCXpHMHp7eTfHQWDxEyyRwNs}
}
|
|||||
| Zhao, W., Serpedin, E. and Dougherty, E.R. | Inferring gene regulatory networks from time series data using the minimum description length principle [BibTeX] |
2006 | Bioinformatics Vol. 22(17), pp. 2129-2135 |
article | |
BibTeX:
@article{zhao_inferring_2006,
author = {Zhao, Wentao and Serpedin, Erchin and Dougherty, Edward R.},
title = {Inferring gene regulatory networks from time series data using the minimum description length principle},
journal = {Bioinformatics},
year = {2006},
volume = {22},
number = {17},
pages = {2129--2135}
}
|
|||||
| Godfrey-Smith, P. | Information in Biology | 2007 | , pp. 103-119 | incollection | URL |
| Abstract: INTRODUCTION The concept of information has acquired a strikingly prominent role in contemporary biology. This trend is especially marked within genetics, but it has also become important in other areas, such as evolutionary theory and developmental biology, especially where these fields border on genetics. The most distinctive biological role for informational concepts, and the one that has generated the most discussion, is in the description of the relations between genes and the various structures and processes that genes play a role in causing. For many biologists, the causal role of genes should be understood in terms of their carrying information about their various products. That information might require the cooperation of various environmental factors before it can be "expressed," but the same can be said of other kinds of message. An initial response might be to think that this mode of description is entirely anchored in a set of well-established facts about the role of DNA and RNA within protein synthesis, summarized in the familiar chart representing the "genetic code," mapping DNA base triplets to amino acids. However, informational enthusiasm in biology predates even a rudimentary understanding of these mechanisms (Schrodinger 1944). And more importantly, current applications of informational concepts extend far beyond anything that can receive an obvious justification in terms of the familiar facts about the specification of protein molecules by DNA. | |||||
BibTeX:
@incollection{godfrey-smith_information_2007,
author = {Godfrey-Smith, Peter},
title = {Information in Biology},
publisher = {Cambridge University Press},
year = {2007},
pages = {103--119},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwjV3LS8MwGP9QQRkKuum6-YDivV3btHkctToHDuZhB2-lzQO8bNNth_33Jm1apzLYMTRpST6a7_n7fQAo8gPvz52AhZIFyXmhklgx7XCHClMiCqoChVVJzLQV2YbBjoR-SAZpOhlbIn5tLGiHwS8Ztw-1JW5IHl-GTYTFkNFRhCxAtZzMyl5B2s3XSpBGln-neZNlgKqf0wbws-Or23QMhmmUzxfr5ZZ2Gp5DXX9cV6U0qeofMP3_qu19d30BpwYQ4RqkghZCGw7krAPHVRPLTQdab3U3hM0ldC28yYjb_Zi5dtYVTIfP03Tk2dYLHk8o8-K8iGXEqD5CxJJASANVwETFBUo4KSIsOY54QUIeYspzlVN9cySMCREQiQhFXTjLTYX-bFUi-YQDR6uvtXSMhnP06Thw8s7GT3T0mlbDdj30lyXazP9cOVqhlj-jh33SAzfOEdfWqAoM9peY9C0PEm2hSixkkoeiD_eNODLO51n6OPklzwfte_ahV8kpW1RsHhk26GRjal7vs_4GWlV01wRhbqtd3VUUjt_bfsJq}
}
|
|||||
| Sarkar, S. | Information in Genetics and Developmental Biology: Comments on Maynard Smith [BibTeX] |
2000 | Philosophy of Science Vol. 67(2), pp. 208-213 |
article | |
BibTeX:
@article{sarkar_information_2000,
author = {Sarkar, Sahotra},
title = {Information in Genetics and Developmental Biology: Comments on Maynard Smith},
journal = {Philosophy of Science},
year = {2000},
volume = {67},
number = {2},
pages = {208--213}
}
|
|||||
| Adami, C. | Information theory in molecular biology | 2004 | Physics of Life Reviews Vol. 1(1), pp. 3-22 |
article | |
| Abstract: This article introduces the physics of information in the context of molecular biology and genomics. Entropy and information, the two central concepts of Shannon's theory of information and communication, are often confused with each other but play transparent roles when applied to statistical ensembles (i.e., identically prepared sets) of symbolic sequences. Such an approach can distinguish between entropy and information in genes, predict the secondary structure of ribozymes, and detect the covariation between residues in folded proteins. We also review applications to molecular sequence and structure analysis, and introduce new tools in the characterization of resistance mutations, and in drug design. © 2004 Elsevier B.V. All rights reserved.;This article introduces the physics of information in the context of molecular biology and genomics. Entropy and information, the two central concepts of Shannon's theory of information and communication, are often confused with each other but play transparent roles when applied to statistical ensembles (i.e., identically prepared sets) of symbolic sequences. Such an approach can distinguish between entropy and information in genes, predict the secondary structure of ribozymes, and detect the covariation between residues in folded proteins. We also review applications to molecular sequence and structure analysis, and introduce new tools in the characterization of resistance mutations, and in drug design.;This article introduces the physics of information in the context of molecular biology and genomics. Entropy and information, the two central concepts of Shannon's theory of information and communication, are often confused with each other but play transparent roles when applied to statistical ensembles (i.e., identically prepared sets) of symbolic sequences. Such an approach can distinguish between entropy and information in genes, predict the secondary structure of ribozymes, and detect the covariation between residues in folded proteins. We also review applications to molecular sequence and structure analysis, and introduce new tools in the characterization of resistance mutations, and in drug design. (c) 2004 Elsevier B.V. All rights reserved.; | |||||
BibTeX:
@article{adami_information_2004,
author = {Adami, Christoph},
title = {Information theory in molecular biology},
journal = {Physics of Life Reviews},
year = {2004},
volume = {1},
number = {1},
pages = {3--22}
}
|
|||||
| Godfrey-Smith, P. | Information, Arbitrariness, and Selection: Comments on Maynard Smith [BibTeX] |
2000 | Philosophy of Science Vol. 67(2), pp. 202-207 |
article | |
BibTeX:
@article{godfrey-smith_information_2000,
author = {Godfrey-Smith, Peter},
title = {Information, Arbitrariness, and Selection: Comments on Maynard Smith},
journal = {Philosophy of Science},
year = {2000},
volume = {67},
number = {2},
pages = {202--207}
}
|
|||||
| Hodgson, G.M. and Knudsen, T. | Information, complexity and generative replication | 2008 | Biology & Philosophy Vol. 23(1), pp. 47-65 |
article | URL |
| Abstract: The established definition of replication in terms of the conditions of causality, similarity and information transfer is very broad. We draw inspiration from the literature on self-reproducing automata to strengthen the notion of information transfer in replication processes. To the triple conditions of causality, similarity and information transfer, we add a fourth condition that defines a “generative replicator” as a conditional generative mechanism, which can turn input signals from an environment into developmental instructions. Generative replication must have the potential to enhance complexity, which in turn requires that developmental instructions are part of the information that is transmitted in replication. Demonstrating the usefulness of the generative replicator concept in the social domain, we identify social generative replicators that satisfy all of the four proposed conditions.; The established definition of replication in terms of the conditions of causality, similarity and information transfer is very broad. We draw inspiration from the literature on self-reproducing automata to strengthen the notion of information transfer in replication processes. To the triple conditions of causality, similarity and information transfer, we add a fourth condition that defines a "generative replicator" as a conditional generative mechanism, which can turn input signals from an environment into developmental instructions. Generative replication must have the potential to enhance complexity, which in turn requires that developmental instructions are part of the information that is transmitted in replication. Demonstrating the usefulness of the generative replicator concept in the social domain, we identify social generative replicators that satisfy all of the four proposed conditions. | |||||
BibTeX:
@article{hodgson_information_2008,
author = {Hodgson, Geoffrey M. and Knudsen, Thorbjørn},
title = {Information, complexity and generative replication},
journal = {Biology & Philosophy},
year = {2008},
volume = {23},
number = {1},
pages = {47--65},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlR3LbtQwcIRAoEoV0AJpCkg5wAU1UWxvEvuIFqpKcEC8xM2yY5sD1artplL37_HYcZouPZRbLE0SxzOZ9wOA0aout3gC76wWgmraM2NE6-jCtd0CWaRrbBOaf84820AnT8bqT5UClIFvz0rfGiZKdLR5846VG8-FvahCGv_67efEi1Hax-7eomS87VJc87Yn3JRMM3UT60Mu17NQ6a1CKgik4yeQCmVSIsoUnb6un_83Ufs_PvQpPB511eJ9JK49uGdX-_AwTq_c7MPOlzQGYfMM6FjXhHg-KkKiur3yGn6hVqb4HXpbI2MtLuwUMH8OP44_fl-elOM8hrInXksqWW0osWrhjCZU9V53sA03RhsnhO5bI6hfELtQhGjPSbjDMR7OCGf7Vte9Yy9gV2He_moI9X0mgwfO_2Q2Q8GX-RPM4NEv8fkDP_m0jMu9tKzWoQitOh8yj9vwj5Zt1R1A4bwGYhRpueLWUxTTWjHmjbjWGtUq7nJ4l9Aqz2IHD3ndqxkPV-IlHq7c5JAlxEtzeuoNI69PUjQbc3gb6WB6CJVrKmvJ0ML1VhnnjRyuhhwOtuAwdItmY5fDUULxbCe4AXQYyxGbcSdnxuEbt8HD0NDxHiZJgM3hzZwaJ9g62I_Y9xWVEg9G7gK2HFvDY0uE4fCOW3gJOzGPBl1Tr-D-cHFpX8fGln8BjQMrmg}
}
|
|||||
| Hodgson, G.M. and Knudsen, T. | Information, complexity and generative replication | 2008 | Biology & Philosophy Vol. 23(1), pp. 47-65 |
article | URL |
| Abstract: The established definition of replication in terms of the conditions of causality, similarity and information transfer is very broad. We draw inspiration from the literature on self-reproducing automata to strengthen the notion of information transfer in replication processes. To the triple conditions of causality, similarity and information transfer, we add a fourth condition that defines a “generative replicator” as a conditional generative mechanism, which can turn input signals from an environment into developmental instructions. Generative replication must have the potential to enhance complexity, which in turn requires that developmental instructions are part of the information that is transmitted in replication. Demonstrating the usefulness of the generative replicator concept in the social domain, we identify social generative replicators that satisfy all of the four proposed conditions.; The established definition of replication in terms of the conditions of causality, similarity and information transfer is very broad. We draw inspiration from the literature on self-reproducing automata to strengthen the notion of information transfer in replication processes. To the triple conditions of causality, similarity and information transfer, we add a fourth condition that defines a "generative replicator" as a conditional generative mechanism, which can turn input signals from an environment into developmental instructions. Generative replication must have the potential to enhance complexity, which in turn requires that developmental instructions are part of the information that is transmitted in replication. Demonstrating the usefulness of the generative replicator concept in the social domain, we identify social generative replicators that satisfy all of the four proposed conditions. | |||||
BibTeX:
@article{hodgson_information_2008,
author = {Hodgson, Geoffrey M. and Knudsen, Thorbjørn},
title = {Information, complexity and generative replication},
journal = {Biology & Philosophy},
year = {2008},
volume = {23},
number = {1},
pages = {47--65},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlR3LbtQwcIRAoEoV0AJpCkg5wAU1UWxvEvuIFqpKcEC8xM2yY5sD1artplL37_HYcZouPZRbLE0SxzOZ9wOA0aout3gC76wWgmraM2NE6-jCtd0CWaRrbBOaf84820AnT8bqT5UClIFvz0rfGiZKdLR5846VG8-FvahCGv_67efEi1Hax-7eomS87VJc87Yn3JRMM3UT60Mu17NQ6a1CKgik4yeQCmVSIsoUnb6un_83Ufs_PvQpPB511eJ9JK49uGdX-_AwTq_c7MPOlzQGYfMM6FjXhHg-KkKiur3yGn6hVqb4HXpbI2MtLuwUMH8OP44_fl-elOM8hrInXksqWW0osWrhjCZU9V53sA03RhsnhO5bI6hfELtQhGjPSbjDMR7OCGf7Vte9Yy9gV2He_moI9X0mgwfO_2Q2Q8GX-RPM4NEv8fkDP_m0jMu9tKzWoQitOh8yj9vwj5Zt1R1A4bwGYhRpueLWUxTTWjHmjbjWGtUq7nJ4l9Aqz2IHD3ndqxkPV-IlHq7c5JAlxEtzeuoNI69PUjQbc3gb6WB6CJVrKmvJ0ML1VhnnjRyuhhwOtuAwdItmY5fDUULxbCe4AXQYyxGbcSdnxuEbt8HD0NDxHiZJgM3hzZwaJ9g62I_Y9xWVEg9G7gK2HFvDY0uE4fCOW3gJOzGPBl1Tr-D-cHFpX8fGln8BjQMrmg}
}
|
|||||
| Adami, C. | Information-Theoretic Considerations Concerning the Origin of Life | 2015 | Origins of Life and Evolution of Biospheres Vol. 45(3), pp. 309-317 |
article | |
| Abstract: Research investigating the origins of life usually either focuses on exploring possible life-bearing chemistries in the pre-biotic Earth, or else on synthetic approaches. Comparatively little work has explored fundamental issues concerning the spontaneous emergence of life using only concepts (such as information and evolution) that are divorced from any particular chemistry. Here, I advocate studying the probability of spontaneous molecular self-replication as a function of the information contained in the replicator, and the environmental conditions that might enable this emergence. I show (under certain simplifying assumptions) that the probability to discover a self-replicator by chance depends exponentially on the relative rate of formation of the monomers. If the rate at which monomers are formed is somewhat similar to the rate at which they would occur in a self-replicating polymer, the likelihood to discover such a replicator by chance is increased by many orders of magnitude. I document such an increase in searches for a self-replicator within the digital life system avida.;Research investigating the origins of life usually focuses on exploring possible life-bearing chemistries in the pre-biotic Earth, or else on synthetic approaches. Little work has been done exploring fundamental issues concerning the spontaneous emergence of life using only concepts (such as information and evolution) that are divorced from any particular chemistry. Here, I advocate studying the probability of spontaneous molecular self-replication as a function of the information contained in the replicator, and the environmental conditions that might enable this emergence. I show that (under certain simplifying assumptions) the probability to discover a self-replicator by chance depends exponentially on the rate of formation of the monomers. If the rate at which monomers are formed is somewhat similar to the rate at which they would occur in a self-replicating polymer, the likelihood to discover such a replicator by chance is increased by many orders of magnitude. I document such an increase in searches for a self-replicator within the digital life system avida; Research investigating the origins of life usually either focuses on exploring possible life-bearing chemistries in the pre-biotic Earth, or else on synthetic approaches. Comparatively little work has explored fundamental issues concerning the spontaneous emergence of life using only concepts (such as information and evolution) that are divorced from any particular chemistry. Here, I advocate studying the probability of spontaneous molecular self-replication as a function of the information contained in the replicator, and the environmental conditions that might enable this emergence. I show (under certain simplifying assumptions) that the probability to discover a self-replicator by chance depends exponentially on the relative rate of formation of the monomers. If the rate at which monomers are formed is somewhat similar to the rate at which they would occur in a self-replicating polymer, the likelihood to discover such a replicator by chance is increased by many orders of magnitude. I document such an increase in searches for a self-replicator within the digital life system avida.;Research investigating the origins of life usually either focuses on exploring possible life-bearing chemistries in the pre-biotic Earth, or else on synthetic approaches. Comparatively little work has explored fundamental issues concerning the spontaneous emergence of life using only concepts (such as information and evolution) that are divorced from any particular chemistry. Here, I advocate studying the probability of spontaneous molecular self-replication as a function of the information contained in the replicator, and the environmental conditions that might enable this emergence. I show (under certain simplifying assumptions) that the probability to discover a self-replicator by chance depends exponentially on the relative rate of formation of the monomers. If the rate at which monomers are formed is somewhat similar to the rate at which they would occur in a self-replicating polymer, the likelihood to discover such a replicator by chance is increased by many orders of magnitude. I document such an increase in searches for a self-replicator within the digital life system avida.;Research investigating the origins of life usually either focuses on exploring possible life-bearing chemistries in the pre-biotic Earth, or else on synthetic approaches. Comparatively little work has explored fundamental issues concerning the spontaneous emergence of life using only concepts (such as information and evolution) that are divorced from any particular chemistry. Here, I advocate studying the probability of spontaneous molecular self-replication as a function of the information contained in the replicator, and the environmental conditions that might enable this emergence. I show (under certain simplifying assumptions) that the probability to discover a self-replicator by chance depends exponentially on the relative rate of formation of the monomers. If the rate at which monomers are formed is somewhat similar to the rate at which they would occur in a self-replicating polymer, the likelihood to discover such a replicator by chance is increased by many orders of magnitude. I document such an increase in searches for a self-replicator within the digital life system avida.; | |||||
BibTeX:
@article{adami_information-theoretic_2015,
author = {Adami, Christoph},
title = {Information-Theoretic Considerations Concerning the Origin of Life},
journal = {Origins of Life and Evolution of Biospheres},
year = {2015},
volume = {45},
number = {3},
pages = {309--317}
}
|
|||||
| Barbieri, M. | Introduction to Code Biology [BibTeX] |
2014 | Biosemiotics Vol. 7(2), pp. 167-179 |
article | |
BibTeX:
@article{barbieri_introduction_2014,
author = {Barbieri, Marcello},
title = {Introduction to Code Biology},
journal = {Biosemiotics},
year = {2014},
volume = {7},
number = {2},
pages = {167--179}
}
|
|||||
| Frieden, B.R. | Introduction to Fisher information: Its origin, uses, and predictions [BibTeX] |
2007 | , pp. 1-41 | incollection | |
BibTeX:
@incollection{frieden_introduction_2007,
author = {Frieden, B. R.},
title = {Introduction to Fisher information: Its origin, uses, and predictions},
year = {2007},
pages = {1--41}
}
|
|||||
| Xia, J., Flynn, W.F., Gallicchio, E., Zhang, B.W., He, P., Tan, Z. and Levy, R.M. | Large‐scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis | 2015 | Journal of Computational Chemistry Vol. 36(23), pp. 1772-1785 |
article | URL |
| Abstract: We describe methods to perform replica exchange molecular dynamics (REMD) simulations asynchronously (ASyncRE). The methods are designed to facilitate large scale REMD simulations on grid computing networks consisting of heterogeneous and distributed computing environments as well as on homogeneous high-performance clusters. We have implemented these methods on NSF (National Science Foundation) XSEDE (Extreme Science and Engineering Discovery Environment) clusters and BOINC (Berkeley Open Infrastructure for Network Computing) distributed computing networks at Temple University and Brooklyn College at CUNY (the City University of New York). They are also being implemented on the IBM World Community Grid. To illustrate the methods, we have performed extensive (more than 60 ms in aggregate) simulations for the beta-cyclodextrin-heptanoate host-guest system in the context of one- and two-dimensional ASyncRE, and we used the results to estimate absolute binding free energies using the binding energy distribution analysis method. We propose ways to improve the efficiency of REMD simulations: these include increasing the number of exchanges attempted after a specified molecular dynamics (MD) period up to the fast exchange limit and/or adjusting the MD period to allow sufficient internal relaxation within each thermodynamic state. Although ASyncRE simulations generally require long MD periods (textgreaterpicoseconds) per replica exchange cycle to minimize the overhead imposed by heterogeneous computing networks, we found that it is possible to reach an efficiency similar to conventional synchronous REMD, by optimizing the combination of the MD period and the number of exchanges attempted per cycle.; We describe methods to perform replica exchange molecular dynamics (REMD) simulations asynchronously (ASyncRE). The methods are designed to facilitate large scale REMD simulations on grid computing networks consisting of heterogeneous and distributed computing environments as well as on homogeneous high‐performance clusters. We have implemented these methods on NSF (National Science Foundation) XSEDE (Extreme Science and Engineering Discovery Environment) clusters and BOINC (Berkeley Open Infrastructure for Network Computing) distributed computing networks at Temple University and Brooklyn College at CUNY (the City University of New York). They are also being implemented on the IBM World Community Grid. To illustrate the methods, we have performed extensive (more than 60 ms in aggregate) simulations for the beta‐cyclodextrin‐heptanoate host‐guest system in the context of one‐ and two‐dimensional ASyncRE, and we used the results to estimate absolute binding free energies using the binding energy distribution analysis method. We propose ways to improve the efficiency of REMD simulations: these include increasing the number of exchanges attempted after a specified molecular dynamics (MD) period up to the fast exchange limit and/or adjusting the MD period to allow sufficient internal relaxation within each thermodynamic state. Although ASyncRE simulations generally require long MD periods (textgreaterpicoseconds) per replica exchange cycle to minimize the overhead imposed by heterogeneous computing networks, we found that it is possible to reach an efficiency similar to conventional synchronous REMD, by optimizing the combination of the MD period and the number of exchanges attempted per cycle. © 2015 Wiley Periodicals, Inc. The ASyncRE methodology is presented, allowing the performance of large‐scale replica exchange molecular dynamics (REMD) simulations asynchronously on grid computing networks consisting of heterogeneous and distributed computing environments, as well as on homogeneous high performance clusters like NSF XSEDE clusters and BOINC distributed computing networks at Temple University and Brooklyn College at CUNY. Several ways to improve the efficiency of REMD simulations in the context of the ASyncRE methodology are also proposed.; We describe methods to perform replica exchange molecular dynamics (REMD) simulations asynchronously (ASyncRE). The methods are designed to facilitate large scale REMD simulations on grid computing networks consisting of heterogeneous and distributed computing environments as well as on homogeneous high-performance clusters. We have implemented these methods on NSF (National Science Foundation) XSEDE (Extreme Science and Engineering Discovery Environment) clusters and BOINC (Berkeley Open Infrastructure for Network Computing) distributed computing networks at Temple University and Brooklyn College at CUNY (the City University of New York). They are also being implemented on the IBM World Community Grid. To illustrate the methods, we have performed extensive (more than 60 ms in aggregate) simulations for the beta-cyclodextrin-heptanoate host-guest system in the context of one- and two-dimensional ASyncRE, and we used the results to estimate absolute binding free energies using the binding energy distribution analysis method. We propose ways to improve the efficiency of REMD simulations: these include increasing the number of exchanges attempted after a specified molecular dynamics (MD) period up to the fast exchange limit and/or adjusting the MD period to allow sufficient internal relaxation within each thermodynamic state. Although ASyncRE simulations generally require long MD periods (textgreaterpicoseconds) per replica exchange cycle to minimize the overhead imposed by heterogeneous computing networks, we found that it is possible to reach an efficiency similar to conventional synchronous REMD, by optimizing the combination of the MD period and the number of exchanges attempted per cycle.; We describe methods to perform replica exchange molecular dynamics (REMD) simulations asynchronously (ASyncRE). The methods are designed to facilitate large scale REMD simulations on grid computing networks consisting of heterogeneous and distributed computing environments as well as on homogeneous high-performance clusters. We have implemented these methods on NSF (National Science Foundation) XSEDE (Extreme Science and Engineering Discovery Environment) clusters and BOINC (Berkeley Open Infrastructure for Network Computing) distributed computing networks at Temple University and Brooklyn College at CUNY (the City University of New York). They are also being implemented on the IBM World Community Grid. To illustrate the methods, we have performed extensive (more than 60 ms in aggregate) simulations for the beta-cyclodextrin-heptanoate host-guest system in the context of one- and two-dimensional ASyncRE, and we used the results to estimate absolute binding free energies using the binding energy distribution analysis method. We propose ways to improve the efficiency of REMD simulations: these include increasing the number of exchanges attempted after a specified molecular dynamics (MD) period up to the fast exchange limit and/or adjusting the MD period to allow sufficient internal relaxation within each thermodynamic state. Although ASyncRE simulations generally require long MD periods (textgreaterpicoseconds) per replica exchange cycle to minimize the overhead imposed by heterogeneous computing networks, we found that it is possible to reach an efficiency similar to conventional synchronous REMD, by optimizing the combination of the MD period and the number of exchanges attempted per cycle. © 2015 Wiley Periodicals, Inc. | |||||
BibTeX:
@article{xia_largescale_2015,
author = {Xia, Junchao and Flynn, William F. and Gallicchio, Emilio and Zhang, Bin W. and He, Peng and Tan, Zhiqiang and Levy, Ronald M.},
title = {Large‐scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis},
journal = {Journal of Computational Chemistry},
year = {2015},
volume = {36},
number = {23},
pages = {1772--1785},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw3V3NbtQwELaASoCEEOUnLFDJR6RVlo2TOPaBAw2FCnqCVtpb5NiOGrQb2iaVKCcegWfkSRjbcRIWkDhzTLxJlMzn-duZbxCKyWIZbumEKGUULLvRiVlVRpEiIosSpSXlkU4ts9I0s-0nSI3n_gfBH5na7qGGoQUZ6LlorxppaHBNwatJlSvDl2tGXYG_aWsKlWH5dwwd5n8Ek8qb6y-uLXi-8TN05229ufTVc-Y-2jJQ2PZN0dOb_MXddeMjfOox93PmvMBXfdEumNlT8XlE1ZXzr_u00FiH_FbACSlPa5vqPdjU63q4akiC79eNKyD0eY0otYVb6TTVyUFX056OVjv1DAFXyFm2mupvR6DS45TEE20MYCMTyx5lbjrQb1bDsdB-knJhOn23mLmtrX-X527JELJvVC27l7oJTz5eh2ifQcy_s_9hZRqXehcgTh1vmX8FT2m1JC-Gp_wppPk1QrIuzvE9dLcXFn7lMLWLrunmPro1iOoB-mqx9ePbd4sqPEUVBjTgCarwNqpwjyrsUYUHVOEJqux9RlRhj6qH6OTNwXF-GPbDO8IzCDJoqISkSsIXACNSVjRR4CdGccl4VZpBVctY00RTrVlChM64AG0gmWQZKQl45BCYPEJ3hGnyaDrbDKoCtFPBxtSB8ZIC-DgBurniR6_Z4fvcHe76w0VrOxYX510AErH7OqSL7DHCcVIxnYBLTjKRxKQswfxUJQdYcbWEyGCG9rxQClGaZKPs2iKi4LMxw204Q8GwrtbrIs5SDjYM7JpZsTIszhxNTEHA8-U0SWfouRXqsOCYwkkBUCgsFAoPryf__tOn6Pa4a56hG93Fpd5zXKI_ASynuoU}
}
|
|||||
| Chaitin, G. | Life as evolving software [BibTeX] |
2012 | incollection | ||
BibTeX:
@incollection{chaitin_life_2012,
author = {Chaitin, Gregory},
title = {Life as evolving software},
year = {2012}
}
|
|||||
| Godfrey-Smith, P. | Metaphysics and the philosophical imagination | 2012 | Philosophical Studies Vol. 160(1), pp. 97-113 |
article | URL |
| Abstract: Methods and goals in philosophy are discussed by first describing an ideal, and then looking at how the ideal might be approached. David Lewis's work in metaphysics is critically examined and compared to analogous work by Mackie and Carnap. Some large-scale philosophical systematic work, especially in metaphysics, is best treated as model-building, in a sense of that term that draws on the philosophy of science. Models are constructed in a way that involves deliberate simplification, or other imaginative modification of reality, in order to make relationships visible or problems tractable.; Issue Title: Special Issue: Metaphysics and Science Methods and goals in philosophy are discussed by first describing an ideal, and then looking at how the ideal might be approached. David Lewis's work in metaphysics is critically examined and compared to analogous work by Mackie and Carnap. Some large-scale philosophical systematic work, especially in metaphysics, is best treated as model-building, in a sense of that term that draws on the philosophy of science. Models are constructed in a way that involves deliberate simplification, or other imaginative modification of reality, in order to make relationships visible or problems tractable.[PUBLICATION ABSTRACT]; Methods and goals in philosophy are discussed by first describing an ideal, and then looking at how the ideal might be approached. David Lewis’s work in metaphysics is critically examined and compared to analogous work by Mackie and Carnap. Some large-scale philosophical systematic work, especially in metaphysics, is best treated as model-building, in a sense of that term that draws on the philosophy of science. Models are constructed in a way that involves deliberate simplification, or other imaginative modification of reality, in order to make relationships visible or problems tractable. | |||||
BibTeX:
@article{godfrey-smith_metaphysics_2012,
author = {Godfrey-Smith, Peter},
title = {Metaphysics and the philosophical imagination},
journal = {Philosophical Studies},
year = {2012},
volume = {160},
number = {1},
pages = {97--113},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV3db9QwDLcQSGgSGoyPrnxIfQAeED01TZqPR3QwTQIkxJd4i5omlSbGcew6afz32Mm1t932MJ5OPflybuzYcRz_DMDrWVVu2QTTe6fQtztVOWoJ2QbljPGmaloXeNAXT7ahnk4yFj9nY4Iy2u1N6RsjJEw0ryXucHhJ5b7oqkjHP3_5PtliaZqEw8xZqRmTY17zqhEueKZt-0xIot3v5enqXMb0Sl8V_dLBXRjrZcb7KFOSelNGf_m-9n-87z3YXW9ZizdJx_bgRljch51PYw-Evw-g_BiGNp2RrIp24QvcVRbLkYDUoDj6Re2Qoho8hG8H777OD8t1H4ayY1o2pdK8qzrpTK0J0Ut1fa0YAQEG31fCh7qvXNDS91zSfsUrjOlCMEagFe6c4_wR3Gnpvv5iiHV9PoNbPS6ukJHDy3DKMrj9w3x4qw_fz9Pj3vg4W8Xis9mfIUOZxrVZypnah6KvK8EUa_GvhMAgyhmOH51oOoEhnBA5vBrFaZcJucNuMJppNi3OpqXZtDqHjARuaVUPJ21nOcXJRjY4TDbqgPXHxxYDVGq0JCTL4UVSiWn42q5qW1ktNFXsGtFoO5wNOexv0XFJbXU0x8Ffj9Le8BhZq4m3tWATj0vf5_DyEnkkTL9hEl8vEufw_LxmTsQxAlYiZmPR_ObArkM2X6PFE0rC8Pi6PDyBHfo-XZZ8CjeHk9PwLIFd_gN7Ui0Q}
}
|
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| Godfrey-Smith, P. | Misinformation [BibTeX] |
1989 | Canadian Journal of Philosophy Vol. 19(4), pp. 533-550 |
article | URL |
BibTeX:
@article{godfrey-smith_misinformation_1989,
author = {Godfrey-Smith, Peter},
title = {Misinformation},
journal = {Canadian Journal of Philosophy},
year = {1989},
volume = {19},
number = {4},
pages = {533--550},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1LS8QwEB5kTyv43tX6gP0D1SZNkxYEEXHxonjQc8hTlKXW3fXgvzfT1-Lr4CWXFDqThHlkvnwDkNLTJP5mE4IbLphV3AaHZXJFMmW15Rkx3HjMh77ebPc3GQiyrFGCdU0_hEt65s4YUpZxnl9UbzF2j8Iqa9tKI5hiQglS6NO7ojfI4Yg1pOEsi9E_9ta3QSCuw7Dq2gZ8_DDJtZ-ZbkEHbOvwJX3RefUs_hf89T_l34bNNg6dXDYHZwfWXLkLw_tewj3YuH1etLSquHkjeJxeP1zdxG33hPiJcMwwBbfeakZ1iHmIt1ynjisiXMh4mLVEqYw7ViAfDHFGYKDimaFC24Iq5206hkH5WroDmGBx1CemUKkpmKBKO54wnTHBmQ8JShrBCBdUolDLuTIyF3mIpPIIxrX2smqYM2SnegTnqyXvZ1dqmReclojnQtAdDgmT-Gw4DFkSwX63SdLOwnc05MKMBnt1-Ncfj2BYo8NqIMoxDJbzd3fSUC9-Al86yFM}
}
|
|||||
| Shea, N. | Neural Signaling of Probabilistic Vectors | 2014 | Philosophy of Science Vol. 81(5), pp. 902-913 |
article | URL |
| Abstract: Recent work combining cognitive neuroscience with computational modeling suggests that distributed patterns of neural firing may represent probability distributions. This article asks, what makes it the case that distributed patterns of firing, as well as carrying information about (correlating with) probability distributions over worldly parameters, represent such distributions? In examples of probabilistic population coding, it is the way information is used in downstream processing so as to lead to successful behavior. In these cases content depends on factors beyond bare information, contra Brian Skyrms’s view that representational content can be fully characterized in information-theoretic terms.; Recent work combining cognitive neuroscience with computational modeling suggests that distributed patterns of neural firing may represent probability distributions. This article asks, what makes it the case that distributed patterns of firing, as well as carrying information about (correlating with) probability distributions over worldly parameters, represent such distributions? In examples of probabilistic population coding, it is the way information is used in downstream processing so as to lead to successful behavior. In these cases content depends on factors beyond bare information, contra Brian Skyrms's view that representational content can be fully characterized in information-theoretic terms.; Recent work combining cognitive neuroscience with computational modeling suggests that distributed patterns of neural firing may represent probability distributions. This article asks, what makes it the case that distributed patterns of firing, as well as carrying information about (correlating with) probability distributions over worldly parameters, represent such distributions? In examples of probabilistic population coding, it is the way information is used in downstream processing so as to lead to successful behavior. In these cases content depends on factors beyond bare information, contra Brian Skyrms’s view that representational content can be fully characterized in information-theoretic terms.; Recent work combining cognitive neuroscience with computational modeling suggests that distributed patterns of neural firing may represent probability distributions. This article asks, what makes it the case that distributed patterns of firing, as well as carrying information about (correlating with) probability distributions over worldly parameters, represent such distributions? In examples of probabilistic population coding, it is the way information is used in downstream processing so as to lead to successful behavior. In these cases content depends on factors beyond bare information, contra Brian Skyrms's view that representational content can be fully characterized in information-theoretic terms. | |||||
BibTeX:
@article{shea_neural_2014,
author = {Shea, Nicholas},
title = {Neural Signaling of Probabilistic Vectors},
journal = {Philosophy of Science},
year = {2014},
volume = {81},
number = {5},
pages = {902--913},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwjV1LT8MwDLYQSGgSArZBGTDRAwd26FibNEmPaDBNgsPES9yqdmkmJDQeHQf-PU7SdhsPwTFtk6hNbH-p7c8AJOj2vC86IRiHEg1fgnCBIcKVlOtKVJp8KiQZVXT5zza4vzj0BTtl5lcF6lzCiRbE6_6o8hr4omc1L_E9EVCxUEvIdlsyPjb-cBlZ6lSQ9_xrJZIfjZIxQIMtKCtzlYEnlTd6ni__PTD71xfbhs0CibpnduvUYSWbNqA2KksbfDSgXgh-7p4U7NSdJnQ0nQf2u3mcaAw_nbjPyh29oVrQYbaa9dm9N56AfAfuBhe3_aFX1FvwxojKuKdoT7KE4QFDRqHyE8lpkvJQc_RJGUQsUzogMRgTTlmKpi-NCMINkSg8ZkmFQ-zCRqLj8qczk78nHVhTKESZow2bg1_MgfWH6OpcDC_7tlkvm93cJJl1X2cOrqaRQY91-R64sjdWKWHS9xNCeYqQMEOImwVEJTKTkWjBUbmm8Ytl6IiNZ12w2H7TFjTNUle3y8tOufKxfHqKiS637gec-S3Ysxth3kPnmkZC4Gztpa0RFyKfV4MeL26VagBDBBSGXNehRyXYAv8_j_ULnnbNTzDb_2PqA6ghmqM21uYQVmdv71nbskt-AiHJBRk}
}
|
|||||
| Shea, N. | Neural Signaling of Probabilistic Vectors | 2014 | Philosophy of Science Vol. 81(5), pp. 902-913 |
article | URL |
| Abstract: Recent work combining cognitive neuroscience with computational modeling suggests that distributed patterns of neural firing may represent probability distributions. This article asks, what makes it the case that distributed patterns of firing, as well as carrying information about (correlating with) probability distributions over worldly parameters, represent such distributions? In examples of probabilistic population coding, it is the way information is used in downstream processing so as to lead to successful behavior. In these cases content depends on factors beyond bare information, contra Brian Skyrms’s view that representational content can be fully characterized in information-theoretic terms.; Recent work combining cognitive neuroscience with computational modeling suggests that distributed patterns of neural firing may represent probability distributions. This article asks, what makes it the case that distributed patterns of firing, as well as carrying information about (correlating with) probability distributions over worldly parameters, represent such distributions? In examples of probabilistic population coding, it is the way information is used in downstream processing so as to lead to successful behavior. In these cases content depends on factors beyond bare information, contra Brian Skyrms's view that representational content can be fully characterized in information-theoretic terms.; Recent work combining cognitive neuroscience with computational modeling suggests that distributed patterns of neural firing may represent probability distributions. This article asks, what makes it the case that distributed patterns of firing, as well as carrying information about (correlating with) probability distributions over worldly parameters, represent such distributions? In examples of probabilistic population coding, it is the way information is used in downstream processing so as to lead to successful behavior. In these cases content depends on factors beyond bare information, contra Brian Skyrms’s view that representational content can be fully characterized in information-theoretic terms.; Recent work combining cognitive neuroscience with computational modeling suggests that distributed patterns of neural firing may represent probability distributions. This article asks, what makes it the case that distributed patterns of firing, as well as carrying information about (correlating with) probability distributions over worldly parameters, represent such distributions? In examples of probabilistic population coding, it is the way information is used in downstream processing so as to lead to successful behavior. In these cases content depends on factors beyond bare information, contra Brian Skyrms's view that representational content can be fully characterized in information-theoretic terms. | |||||
BibTeX:
@article{shea_neural_2014,
author = {Shea, Nicholas},
title = {Neural Signaling of Probabilistic Vectors},
journal = {Philosophy of Science},
year = {2014},
volume = {81},
number = {5},
pages = {902--913},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwjV1LT8MwDLYQSGgSArZBGTDRAwd26FibNEmPaDBNgsPES9yqdmkmJDQeHQf-PU7SdhsPwTFtk6hNbH-p7c8AJOj2vC86IRiHEg1fgnCBIcKVlOtKVJp8KiQZVXT5zza4vzj0BTtl5lcF6lzCiRbE6_6o8hr4omc1L_E9EVCxUEvIdlsyPjb-cBlZ6lSQ9_xrJZIfjZIxQIMtKCtzlYEnlTd6ni__PTD71xfbhs0CibpnduvUYSWbNqA2KksbfDSgXgh-7p4U7NSdJnQ0nQf2u3mcaAw_nbjPyh29oVrQYbaa9dm9N56AfAfuBhe3_aFX1FvwxojKuKdoT7KE4QFDRqHyE8lpkvJQc_RJGUQsUzogMRgTTlmKpi-NCMINkSg8ZkmFQ-zCRqLj8qczk78nHVhTKESZow2bg1_MgfWH6OpcDC_7tlkvm93cJJl1X2cOrqaRQY91-R64sjdWKWHS9xNCeYqQMEOImwVEJTKTkWjBUbmm8Ytl6IiNZ12w2H7TFjTNUle3y8tOufKxfHqKiS637gec-S3Ysxth3kPnmkZC4Gztpa0RFyKfV4MeL26VagBDBBSGXNehRyXYAv8_j_ULnnbNTzDb_2PqA6ghmqM21uYQVmdv71nbskt-AiHJBRk}
}
|
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| Wolf, Y.I. and Koonin, E.V. | On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization | 2007 | Biology Direct Vol. 2(1), pp. 1-25 |
article | DOI URL |
| Abstract: The origin of the translation system is, arguably, the central and the hardest problem in the study of the origin of life, and one of the hardest in all evolutionary biology. The problem has a clear catch-22 aspect: high translation fidelity hardly can be achieved without a complex, highly evolved set of RNAs and proteins but an elaborate protein machinery could not evolve without an accurate translation system. The origin of the genetic code and whether it evolved on the basis of a stereochemical correspondence between amino acids and their cognate codons (or anticodons), through selectional optimization of the code vocabulary, as a “frozen accident” or via a combination of all these routes is another wide open problem despite extensive theoretical and experimental studies. Here we combine the results of comparative genomics of translation system components, data on interaction of amino acids with their cognate codons and anticodons, and data on catalytic activities of ribozymes to develop conceptual models for the origins of the translation system and the genetic code. | |||||
BibTeX:
@article{wolf_origin_2007,
author = {Wolf, Yuri I. and Koonin, Eugene V.},
title = {On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization},
journal = {Biology Direct},
year = {2007},
volume = {2},
number = {1},
pages = {1--25},
url = {http://dx.doi.org/10.1186/1745-6150-2-14},
doi = {http://doi.org/10.1186/1745-6150-2-14}
}
|
|||||
| Plastino, A., Plastino, A.R. and Miller, H.G. | On the relationship between the Fisher-Frieden-Soffer arrow of time, and the behaviour of the Boltzmann and Kullback entropies [BibTeX] |
1997 | Physics Letters A Vol. 235(2), pp. 129-134 |
article | |
BibTeX:
@article{plastino_relationship_1997,
author = {Plastino, A. and Plastino, A. R. and Miller, H. G.},
title = {On the relationship between the Fisher-Frieden-Soffer arrow of time, and the behaviour of the Boltzmann and Kullback entropies},
journal = {Physics Letters A},
year = {1997},
volume = {235},
number = {2},
pages = {129--134}
}
|
|||||
| Godfrey-Smith, P. | On the Theoretical Role of "Genetic Coding" | 2000 | Philosophy of Science Vol. 67(1), pp. 26-44 |
article | URL |
| Abstract: The role played by the concept of genetic coding in biology is discussed. I argue that this concept makes a real contribution to solving a specific problem in cell biology.; The role played by the concept of genetic coding in biology is discussed. I argue that this concept makes a real contribution to solving a specific problem in cell biology. But attempts to make the idea of genetic coding do theoretical work elsewhere in biology, and in philosophy of biology, are probably mistaken. In particular, the concept of genetic coding should not be used (as it often is) to express a distinction between the traits of whole organisms that are coded for in the genes and the traits that are not.; The role played by the concept of genetic coding in biology is discussed. I argue that this concept makes a real contribution to solving a specific problem in cell biology. But attempts to make the idea of genetic coding do theoretical work elsewhere in biology, and in philosophy of biology, are probably mistaken. In particular, the concept of genetic coding should not be used (as it often is) to express a distinction between the traits of whole organisms that are coded for in the genes and the traits that are not. | |||||
BibTeX:
@article{godfrey-smith_theoretical_2000,
author = {Godfrey-Smith, Peter},
title = {On the Theoretical Role of "Genetic Coding"},
journal = {Philosophy of Science},
year = {2000},
volume = {67},
number = {1},
pages = {26--44},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV3Ni9QwFH-IgiyIOvtRqy6GZQ-KdMxHm6YnkeqyoKDIHLyFtE1Pw8zutgvuf78vSdvZGeag0EvafLTJy3u_9H0BCD6nyQ5PyK0QtqYVCs-qygqLZVYYa4yT8Dw123-2YUxc6IwsvZWg1-kjXKqW9hNTCsXy56vrxOWOcjrWIZEGMmLGaYiSW06qBKZoYMeCJYq7PD8PBNDAhoMp4jbIdF4ht91uUpK98snLoosXMJqVjjYok2J64zq_x0b7v77xJTwfkCr5EkhrBo_s6hAOfo2pD-4OYTYwho68H6JXfziCjz9XBEElWWw8JMnv9dKSdUvOXDW8Rcq1E5lnx7C4-LYoL5MhI0NSc5rxRFaFYNwqw6RB4GcVgqkKD221parJnQ6nEKJBFCVbiWejOme1wqvNeZUbBJsn8Mw4w_1V7x38mgietLjLbOQkX4TzGMHTP8WPr-ryexmKs7E477wX2vy6j3Bl_Vwkcp6_AiJsY9vMmFTi6xS0UllR10WGOBBHxfeN4d244PoqhPDQXvWupEZ0mEsaw4mjA-32dH9jai0FHgSZyGI48kuzaefXJYZoJBTdLJfaYTKEalmRxnC89QTxKE0RAsVwHuhp6onrjmvqdf8IwaXKdP-3x453qgmW5kjTOOTpFh3qgdV00yecP6TLqb0_EyAX98lhKXbD_qVaOcSHd3ER-tf7J-ENHISwBM4e7y087m9u7WkIZnkPVrkuSQ}
}
|
|||||
| Frieden, B.R. and Gatenby, R.A. | Order in a multidimensional system [BibTeX] |
2011 | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics Vol. 84(1), pp. 011128 |
article | |
BibTeX:
@article{frieden_order_2011,
author = {Frieden, B. R. and Gatenby, Robert A.},
title = {Order in a multidimensional system},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
year = {2011},
volume = {84},
number = {1},
pages = {011128}
}
|
|||||
| Yaffe, M.P. | Organelle inheritance in the yeast cell cycle | 1991 | Vol. 1(6) |
book | URL |
| Abstract: Cell proliferation requires the inheritance of subcellular organelles, yet little is known of the molecular basis of this essential process. Recent microscopy studies of the yeast Saccharomyces cerevisiae have characterized the cellular distribution of mitochondria, vacuoles and elements of the endoplasmic reticulum and Golgi complex. In addition, genetic and microscopical approaches have allowed the isolation and analysis of mutants defective in the inheritance of mitochondria and vacuoles. These investigations are leading to the identification of molecular components mediating the movement of organelles into daughter cells and have revealed that the inheritance of organelles is coordinated with other events of the cell division cycle. | |||||
BibTeX:
@book{yaffe_organelle_1991,
author = {Yaffe, Michael P.},
title = {Organelle inheritance in the yeast cell cycle},
year = {1991},
volume = {1},
number = {6},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1LS8QwEB5EEPTiW9cH9KiH2rRJNpur4updPYckTWAvdZH1sP_emabtuiIsLORQQpowkzCPzHwZAF49sPyPTFBlRSDOoH20TmrJ7MTbEBjXXquo1frN9pBcSEmWnSZIEr6V3V1P0fG2mM9mBVri6DqgL4EKDg8ZPRCKtjcd87fHl0E0o7uTasuPUQzg6B5LV46Loe9Ol_ftHLnYoKt-KaLpIfRB3z4BZYhKr3Dz_yRob03gERwQGiJLIYRj2AnNCeylApbLU8hbKCfd_WezhpCECzpE-J2hXZktqS5QRqGBzC9xhTP4mD6_P73mXQGG3JcCvcsggtSx5hPppXC6xuYtD7WKgUUbVRA6TiqH_YE7KWqy3yJqO4reMGU5P4fd5rMJl5Bpy5WscDLhuVDMoZfInK_GUjlWOa9GkPesNvP0zobpE9CIdEO0G12alnojRqD6_TBrDDSoCjb8eZG2b7WOUIQh11dbz3kN-ymFjNoN7C6-vsNtetjxB0Wn37A}
}
|
|||||
| Smith, M.U. | Paul Griffiths and Karola Stotz: Genetics and Philosophy: An Introduction: Cambridge University Press, Cambridge, 2013, ISBN: 9780521173902, 278 pp, price: $ 29.99 (Paperback), $ 90.00 (Hardcover), $ 24.00 (eBook) [BibTeX] |
2014 | Vol. 23(9) |
book | URL |
BibTeX:
@book{smith_paul_2014,
author = {Smith, Mike U.},
title = {Paul Griffiths and Karola Stotz: Genetics and Philosophy: An Introduction: Cambridge University Press, Cambridge, 2013, ISBN: 9780521173902, 278 pp, price: $ 29.99 (Paperback), $ 90.00 (Hardcover), $ 24.00 (eBook)},
year = {2014},
volume = {23},
number = {9},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1LS8QwEB5EQRRB10d9Qi6CCi1t07SNN1HXFT2Iingr0yS9CPWx9aC_3kxfy6oHPaYZWjrTZDoz33wB4KHnu9_2BB5yrVPpEzt7HKsoQVRKGYkGgzwPzHRmG8I-k1E-eV2Bst63J61vxExmA-HIlUkgXGrhs66KvvHbu4d-L-YN6tCXYewmYdjXNX-7w7Rnmi6L1t5muAxdF0yHMulLz5Pm-J8o7H-8xQosUo8DawoDA5gx5Sqd39xiPVZh0C75MTtoeakP1-CSUITsos3yjBmWml0RXgTZXfVcfR4zkiXa53rqpjsk4eOYnZTskiDxuuGqXYf74fn96chtT2JwVSKFa9KIx0bEaL09qhw5KswjEWgb_gS6CApry0hgnhglpPZRFsJYzXOFqUgw1XwDlpAA-2VVN_ZpB-YKu7qMQx7Psdp1YP5RXp-lo6vTZjjoht647j7zXivHGrVenG7sJZvAbOCoohzt_57k9umYG6EDo4rERqiB0P4WHHX2zF4a6o5sQtJMis-s4jNSfCa3YL-zUC8c0nQjGPJM1pLbf5TbgQW63KDRdmG2ens3ew3V4xcMN965}
}
|
|||||
| Romanini, V., Fernández, E. and service) , S.(O. | Peirce and Biosemiotics: A Guess at the Riddle of Life [BibTeX] |
2014 | Vol. 11 |
book | |
BibTeX:
@book{romanini_peirce_2014,
author = {Romanini, Vinicius and Fernández, Eliseo and service), SpringerLink (Online},
title = {Peirce and Biosemiotics: A Guess at the Riddle of Life},
publisher = {Springer Netherlands},
year = {2014},
volume = {11}
}
|
|||||
| Schulte, P. | Perceptual representations: a teleosemantic answer to the breadth-of-application problem | 2015 | Biology & Philosophy Vol. 30(1), pp. 119-136 |
article | URL |
| Abstract: Teleosemantic theories of representation are often criticized as being "too liberal", i.e. as categorizing states as representations which are not representational at all. Recently, a powerful version of this objection has been put forth by Tyler Burge. Focusing on perception, Burge defends the claim that all teleosemantic theories apply too broadly, thereby missing what is distinctive about representation. Contra Burge, I will argue in this paper that there is a teleosemantic account of perceptual states that does not fall prey to this problem, and that we can arrive at this account by combining some of Burge's insights with a producer-oriented version of teleosemantics. The resulting theory turns out to be attractive and perfectly coherent. By contrast, the coherence of Burge's own anti-teleosemantic approach becomes quite doubtful under closer examination–or so I will argue.[PUBLICATION ABSTRACT]; Teleosemantic theories of representation are often criticized as being "too liberal", i.e. as categorizing states as representations which are not representational at all. Recently, a powerful version of this objection has been put forth by Tyler Burge. Focusing on perception, Burge defends the claim that all teleosemantic theories apply too broadly, thereby missing what is distinctive about representation. Contra Burge, I will argue in this paper that there is a teleosemantic account of perceptual states that does not fall prey to this problem, and that we can arrive at this account by combining some of Burge's insights with a producer-oriented version of teleosemantics. The resulting theory turns out to be attractive and perfectly coherent. By contrast, the coherence of Burge's own anti-teleosemantic approach becomes quite doubtful under closer examination-or so I will argue.; Teleosemantic theories of representation are often criticized as being “too liberal”, i.e. as categorizing states as representations which are not representational at all. Recently, a powerful version of this objection has been put forth by Tyler Burge. Focusing on perception, Burge defends the claim that all teleosemantic theories apply too broadly, thereby missing what is distinctive about representation. Contra Burge, I will argue in this paper that there is a teleosemantic account of perceptual states that does not fall prey to this problem, and that we can arrive at this account by combining some of Burge’s insights with a producer-oriented version of teleosemantics. The resulting theory turns out to be attractive and perfectly coherent. By contrast, the coherence of Burge’s own anti-teleosemantic approach becomes quite doubtful under closer examination—or so I will argue. | |||||
BibTeX:
@article{schulte_perceptual_2015,
author = {Schulte, Peter},
title = {Perceptual representations: a teleosemantic answer to the breadth-of-application problem},
journal = {Biology & Philosophy},
year = {2015},
volume = {30},
number = {1},
pages = {119--136},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlR3LbtQwcIRAoEoIaKEhPKQc4IJwtGvnYfeGFqpKcKh4qTcrsWOBWnZLkxX07zsTx2m69FCkvSSaOOOdyTw8LwDB0xnbkAl12bi5VLy0DhW89EMZS4O6sDKOW3n1ZBv4eJKxPE5DgLKX25PSt1xQpo9gCt12RlIYVRXx-Ocv30dZTNred_dWTMiiDHHN61a4qpkm5ibVh6zbSaj0WiXVK6T9hxAKZUIiyhidvqyf_zdR-z82-ggeDLZq8s4z1zbcapY7cNdPrzzfga3DMAbh_DEcHfoMmTU-0DfKDEVNy3YvqZIOtduqbX4hHX-aBNXjn-Ys6VYJmp8JOuWV7X6wlWOTcHoyjLp5At_2P3xdHLBhagMz5Cux3DiHVgm3itdW5VUfGs1nmRFGkfVYFlmel1wUrhJOoX3JlaxQ0tQKfwW3YhfuV5TdTwihvW0juOPwU2wiUo8R_s8R3DtSn97Lg48Lf7kdLtO2L1VLf3cRckD_JbMiLZ9CIou6qma24AY9YllzFFs03KYpMpPhDRPDm0B8fer7fOjLjs5EAo0b0UQCzWOIAntoe3Ki6eyMo0fP5zG89twyLsJ1y_VMS3QMcXcZLqi7vx2usAGXo6UkxTyP4W3ggwki9H5OCAwk94icWkcv3ARHwHx4RuAWetgYXk1ZdoTtGxSVaPapPqgdw_wmYIuhfzz1Teie3RCF57BFt_351Qu43Z2tm5e—UFeNI1Lw}
}
|
|||||
| Schulte, P. | Perceptual representations: a teleosemantic answer to the breadth-of-application problem | 2015 | Biology & Philosophy Vol. 30(1), pp. 119-136 |
article | URL |
| Abstract: Teleosemantic theories of representation are often criticized as being "too liberal", i.e. as categorizing states as representations which are not representational at all. Recently, a powerful version of this objection has been put forth by Tyler Burge. Focusing on perception, Burge defends the claim that all teleosemantic theories apply too broadly, thereby missing what is distinctive about representation. Contra Burge, I will argue in this paper that there is a teleosemantic account of perceptual states that does not fall prey to this problem, and that we can arrive at this account by combining some of Burge's insights with a producer-oriented version of teleosemantics. The resulting theory turns out to be attractive and perfectly coherent. By contrast, the coherence of Burge's own anti-teleosemantic approach becomes quite doubtful under closer examination–or so I will argue.[PUBLICATION ABSTRACT]; Teleosemantic theories of representation are often criticized as being "too liberal", i.e. as categorizing states as representations which are not representational at all. Recently, a powerful version of this objection has been put forth by Tyler Burge. Focusing on perception, Burge defends the claim that all teleosemantic theories apply too broadly, thereby missing what is distinctive about representation. Contra Burge, I will argue in this paper that there is a teleosemantic account of perceptual states that does not fall prey to this problem, and that we can arrive at this account by combining some of Burge's insights with a producer-oriented version of teleosemantics. The resulting theory turns out to be attractive and perfectly coherent. By contrast, the coherence of Burge's own anti-teleosemantic approach becomes quite doubtful under closer examination-or so I will argue.; Teleosemantic theories of representation are often criticized as being “too liberal”, i.e. as categorizing states as representations which are not representational at all. Recently, a powerful version of this objection has been put forth by Tyler Burge. Focusing on perception, Burge defends the claim that all teleosemantic theories apply too broadly, thereby missing what is distinctive about representation. Contra Burge, I will argue in this paper that there is a teleosemantic account of perceptual states that does not fall prey to this problem, and that we can arrive at this account by combining some of Burge’s insights with a producer-oriented version of teleosemantics. The resulting theory turns out to be attractive and perfectly coherent. By contrast, the coherence of Burge’s own anti-teleosemantic approach becomes quite doubtful under closer examination—or so I will argue. | |||||
BibTeX:
@article{schulte_perceptual_2015,
author = {Schulte, Peter},
title = {Perceptual representations: a teleosemantic answer to the breadth-of-application problem},
journal = {Biology & Philosophy},
year = {2015},
volume = {30},
number = {1},
pages = {119--136},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlR3LbtQwcIRAoEoIaKEhPKQc4IJwtGvnYfeGFqpKcKh4qTcrsWOBWnZLkxX07zsTx2m69FCkvSSaOOOdyTw8LwDB0xnbkAl12bi5VLy0DhW89EMZS4O6sDKOW3n1ZBv4eJKxPE5DgLKX25PSt1xQpo9gCt12RlIYVRXx-Ocv30dZTNred_dWTMiiDHHN61a4qpkm5ibVh6zbSaj0WiXVK6T9hxAKZUIiyhidvqyf_zdR-z82-ggeDLZq8s4z1zbcapY7cNdPrzzfga3DMAbh_DEcHfoMmTU-0DfKDEVNy3YvqZIOtduqbX4hHX-aBNXjn-Ys6VYJmp8JOuWV7X6wlWOTcHoyjLp5At_2P3xdHLBhagMz5Cux3DiHVgm3itdW5VUfGs1nmRFGkfVYFlmel1wUrhJOoX3JlaxQ0tQKfwW3YhfuV5TdTwihvW0juOPwU2wiUo8R_s8R3DtSn97Lg48Lf7kdLtO2L1VLf3cRckD_JbMiLZ9CIou6qma24AY9YllzFFs03KYpMpPhDRPDm0B8fer7fOjLjs5EAo0b0UQCzWOIAntoe3Ki6eyMo0fP5zG89twyLsJ1y_VMS3QMcXcZLqi7vx2usAGXo6UkxTyP4W3ggwki9H5OCAwk94icWkcv3ARHwHx4RuAWetgYXk1ZdoTtGxSVaPapPqgdw_wmYIuhfzz1Teie3RCF57BFt_351Qu43Z2tm5e—UFeNI1Lw}
}
|
|||||
| Godfrey-Smith, P. | Philosophy of biology [BibTeX] |
2013 | book | ||
BibTeX:
@book{godfrey-smith_philosophy_2013,
author = {Godfrey-Smith, Peter},
title = {Philosophy of biology},
publisher = {Princeton University Press},
year = {2013}
}
|
|||||
| Frieden, B.R. and Gatenby, R.A. | Power laws of complex systems from extreme physical information | 2005 | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics Vol. 72(3), pp. 036101 |
article | URL |
| Abstract: Many complex systems obey allometric, or power, laws y=Y x(a) . Here y textgreater or = 0 is the measured value of some system attribute a , Ytextgreater or =0 is a constant, and x is a stochastic variable. Remarkably, for many living systems the exponent a is limited to values n/4 , n=0, +/-1, +/-2... Here x is the mass of a randomly selected creature in the population. These quarter-power laws hold for many attributes, such as pulse rate (n=-1) . Allometry has, in the past, been theoretically justified on a case-by-case basis. An ultimate goal is to find a common cause for allometry of all types and for both living and nonliving systems. The principle I-J=extremum of extreme physical information is found to provide such a cause. It describes the flow of Fisher information J–textgreaterI from an attribute value a on the cell level to its exterior observation y . Data y are formed via a system channel function y identical to f (x,a) , with f (x,a) to be found. Extremizing the difference I-J through variation of f (x,a) results in a general allometric law f (x,a) identical to y=Y x(a) . Darwinian evolution is presumed to cause a second extremization of I-J , now with respect to the choice of a . The solution is a=n/4 , n=0,+/-1,+/-2..., defining the particular powers of biological allometry. Under special circumstances, the model predicts that such biological systems are controlled by only two distinct intracellular information sources. These sources are conjectured to be cellular DNA and cellular transmembrane ion gradients.; Many complex systems obey allometric, or power, laws y=Yx(a). Here y textgreater= 0 is the measured value of some system attribute a, Y textgreater= 0 is a constant, and x is a stochastic variable. Remarkably, for many living systems the exponent a is limited to values n/4, n=0,+/- 1,+/- 2,... Here x is the mass of a randomly selected creature in the population. These quarter-power laws hold for many attributes, such as pulse rate (n=-1). Allometry has, in the past, been theoretically justified on a case-by-case basis. An ultimate goal is to find a common cause for allometry of all types and for both living and nonliving systems. The principle I-J=extremum of extreme physical information is found to provide such a cause. It describes the flow of Fisher information J -textgreater I from an attribute value a on the cell level to its exterior observation y. Data y are formed via a system channel function y equivalent to f(x,a), with f(x,a) to be found. Extremizing the difference I-J through variation of f(x,a) results in a general allometric law f(x,a)equivalent to y=Yx(a). Darwinian evolution is presumed to cause a second extremization of I-J, now with respect to the choice of a. The solution is a=n/4, n=0,+/- 1,+/- 2..., defining the particular powers of biological allometry. Under special circumstances, the model predicts that such biological systems are controlled by only two distinct intracellular information sources. These sources are conjectured to be cellular DNA and cellular transmembrane ion gradients. | |||||
BibTeX:
@article{frieden_power_2005,
author = {Frieden, B. R. and Gatenby, Robert A.},
title = {Power laws of complex systems from extreme physical information},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
year = {2005},
volume = {72},
number = {3},
pages = {036101},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1dT9YwFD4hosbEoCjOoSS90CvdWD-2rlfEvEJI1MQYTbhbun5cET7cEH4-p-32Ivhe4GXTrlt72p7T9nmeAXBWVsWdNUFz66w1VjlmuW6oY8IK18teeiqYdLdPtuHj6gt9WvHdAIz84f7slxJfw9H5R-Y6BuGBvvHtaF6FOboikbRSFU6iup4JMyuruOWUlp7oYSCGXAwrXVJ0PwfPYEbfz7CT5V30DVv-X1j2vZr1HDammJR8SoNoE9bcyQt4FLGhZngJe9_Dn9TIsb4cyKknEYTurkjSgB5IIKgQXOLDQSM5m8xOJkHWYPYt-HWw_3NxWEz_XSg0bRpVaEtZ73zLZNX31PHGqLb2tTaaitpiiOeNxP1ri6Ekk4wpai3zmlkpjTCBqPsKnuqAzz8ZI4_PZrDucTK5LDi4DPsug8dH6uvn9vDLIiU352Q5RLJZeT5maMk4F4umlK-BsF55Y02trbJC91r1-C0MNwfcswZXqhw-zDbszpJSRxd3OBXv5t7tJOtS7-aQJTPflG1CMFOpHN4nuy9zWDfgYx1rWyGwzUqobrwasYY75QSVUUAsh3d_D5hlfhQXitzjGJnnQO9TbDFptQeNgnH7vxr5Bp5EpdkIiXsLD8bfF24n6U1eA5myDTI}
}
|
|||||
| Frieden, B. and Gatenby, R. | Principle of maximum Fisher information from Hardy's axioms applied to statistical systems | 2013 | PHYSICAL REVIEW E Vol. 88(4), pp. 042144 |
article | URL |
| Abstract: Consider a finite-sized, multidimensional system in parameter state a. The system is either at statistical equilibrium or general nonequilibrium, and may obey either classical or quantum physics. L. Hardy's mathematical axioms provide a basis for the physics obeyed by any such system. One axiom is that the number N of distinguishable states a in the system obeys N = max. This assumes that N is known as deterministic prior knowledge. However, most observed systems suffer statistical fluctuations, for which N is therefore only known approximately. Then what happens if the scope of the axiom N = max is extended to include such observed systems? It is found that the state a of the system must obey a principle of maximum Fisher information, I = I-max. This is important because many physical laws have been derived, assuming as a working hypothesis that I = I-max. These derivations include uses of the principle of extreme physical information (EPI). Examples of such derivations were of the De Broglie wave hypothesis, quantum wave equations, Maxwell's equations, new laws of biology (e. g., of Coulomb force-directed cell development and of in situ cancer growth), and new laws of economic fluctuation and investment. That the principle I = I-max itself derives from suitably extended Hardy axioms thereby eliminates its need to be assumed in these derivations. Thus, uses of I = I-max and EPI express physics at its most fundamental level, its axiomatic basis in math.; Consider a finite-sized, multidimensional system in parameter state a. The system is either at statistical equilibrium or general nonequilibrium, and may obey either classical or quantum physics. L. Hardy's mathematical axioms provide a basis for the physics obeyed by any such system. One axiom is that the number N of distinguishable states a in the system obeys N=max. This assumes that N is known as deterministic prior knowledge. However, most observed systems suffer statistical fluctuations, for which N is therefore only known approximately. Then what happens if the scope of the axiom N=max is extended to include such observed systems? It is found that the state a of the system must obey a principle of maximum Fisher information, I=I(max). This is important because many physical laws have been derived, assuming as a working hypothesis that I=I(max). These derivations include uses of the principle of extreme physical information (EPI). Examples of such derivations were of the De Broglie wave hypothesis, quantum wave equations, Maxwell's equations, new laws of biology (e.g., of Coulomb force-directed cell development and of in situ cancer growth), and new laws of economic fluctuation and investment. That the principle I=I(max) itself derives from suitably extended Hardy axioms thereby eliminates its need to be assumed in these derivations. Thus, uses of I=I(max) and EPI express physics at its most fundamental level, its axiomatic basis in math. | |||||
BibTeX:
@article{frieden_principle_2013,
author = {Frieden, BR and Gatenby, RA},
title = {Principle of maximum Fisher information from Hardy's axioms applied to statistical systems},
journal = {PHYSICAL REVIEW E},
year = {2013},
volume = {88},
number = {4},
pages = {042144},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV3PS8MwFH6IKAjib139ATkIHnQzTZqsPcrY8CKIKIiXkmQJeNgmthP_fF-atTrdYZ56aGjTvPS970ve-wLAWYe2f_kEZq0S1BqlnMIAZh1H4qGt5HzYTazQ8yvbcLV4Qz-m_NonRj7Yjz5auIMTDvmAr1xHEO7LN-6eay_MMRQlQSs1w59IiLpgZuEj5oJSE4nWfGHItFgYkqrwM9iGOvu-Tjtp9qK_q-X_pmUv9Vk7sDXDpOQmTKJdWLHjPVivckNNsQ8v9_WCPJk4MlKfr6PpiIQz08lMeNWbl_hSFVKlAlwUBJtNRngJKJeUE-JrlypZaHxXEJAuDuBp0H_s3bZnRzK0FQK3pG0kVTLzvNZpqzKjJEWEo7Qw6DS5MDK1qXbSxMqmXYSeItNx3FVpNtTUIfPih7CpfOr-uKxK_IYtIFQjjWKCUUNdkhiaZo4ZxajQWirnkggua-Pkb0GCI6-oC-V5PWx5muZh2CI4CvZr2iIIYdgTFkErGLS5w7uIcHhGZQTnP03cNPCMESkm-qiKS0UQL9OsN1NX96oC5fG_en8CG8yft1FlC57Cavk-tWdBIfILtoT63A}
}
|
|||||
| Altschul, S.F., Gertz, E.M., Agarwala, R., Schäffer, A.A. and Yu, Y.-K. | PSI-BLAST pseudocounts and the minimum description length principle | 2009 | Nucleic acids research Vol. 37(3), pp. 815-824 |
article | URL |
| Abstract: Position specific score matrices (PSSMs) are derived from multiple sequence alignments to aid in the recognition of distant protein sequence relationships. The PSI-BLAST protein database search program derives the column scores of its PSSMs with the aid of pseudocounts, added to the observed amino acid counts in a multiple alignment column. In the absence of theory, the number of pseudocounts used has been a completely empirical parameter. This article argues that the minimum description length principle can motivate the choice of this parameter. Specifically, for realistic alignments, the principle supports the practice of using a number of pseudocounts essentially independent of alignment size. However, it also implies that more highly conserved columns should use fewer pseudocounts, increasing the inter-column contrast of the implied PSSMs. A new method for calculating pseudocounts that significantly improves PSI-BLAST's; retrieval accuracy is now employed by default.; Position specific score matrices (PSSMs) are derived from multiple sequence alignments to aid in the recognition of distant protein sequence relationships. The PSI-BLAST protein database search program derives the column scores of its PSSMs with the aid of pseudocounts, added to the observed amino acid counts in a multiple alignment column. In the absence of theory, the number of pseudocounts used has been a completely empirical parameter. This article argues that the minimum description length principle can motivate the choice of this parameter. Specifically, for realistic alignments, the principle supports the practice of using a number of pseudocounts essentially independent of alignment size. However, it also implies that more highly conserved columns should use fewer pseudocounts, increasing the inter-column contrast of the implied PSSMs. A new method for calculating pseudocounts that significantly improves PSI-BLAST's retrieval accuracy is now employed by default.; Position specific score matrices (PSSMs) are derived from multiple sequence alignments to aid in the recognition of distant protein sequence relationships. The PSI-BLAST protein database search program derives the column scores of its PSSMs with the aid of pseudocounts, added to the observed amino acid counts in a multiple alignment column. In the absence of theory, the number of pseudocounts used has been a completely empirical parameter. This article argues that the minimum description length principle can motivate the choice of this parameter. Specifically, for realistic alignments, the principle supports the practice of using a number of pseudocounts essentially independent of alignment size. However, it also implies that more highly conserved columns should use fewer pseudocounts, increasing the inter-column contrast of the implied PSSMs. A new method for calculating pseudocounts that significantly improves PSI-BLAST's; retrieval accuracy is now employed by default.; Position specific score matrices (PSSMs) are derived from multiple sequence alignments to aid in the recognition of distant protein sequence relationships. The PSI-BLAST protein database search program derives the column scores of its PSSMs with the aid of pseudocounts, added to the observed amino acid counts in a multiple alignment column. In the absence of theory, the number of pseudocounts used has been a completely empirical parameter. This article argues that the minimum description length principle can motivate the choice of this parameter. Specifically, for realistic alignments, the principle supports the practice of using a number of pseudocounts essentially independent of alignment size. However, it also implies that more highly conserved columns should use fewer pseudocounts, increasing the inter-column contrast of the implied PSSMs. A new method for calculating pseudocounts that significantly improves PSI-BLAST's; retrieval accuracy is now employed by default.; Position specific score matrices (PSSMs) are derived from multiple sequence alignments to aid in the recognition of distant protein sequence relationships. The PSI-BLAST protein database search program derives the column scores of its PSSMs with the aid of pseudocounts, added to the observed amino acid counts in a multiple alignment column. In the absence of theory, the number of pseudocounts used has been a completely empirical parameter. This article argues that the minimum description length principle can motivate the choice of this parameter. Specifically, for realistic alignments, the principle supports the practice of using a number of pseudocounts essentially independent of alignment size. However, it also implies that more highly conserved columns should use fewer pseudocounts, increasing the inter-column contrast of the implied PSSMs. A new method for calculating pseudocounts that significantly improves PSI-BLAST's; retrieval accuracy is now employed by default. | |||||
BibTeX:
@article{altschul_psi-blast_2009,
author = {Altschul, Stephen F. and Gertz, E. M. and Agarwala, Richa and Schäffer, Alejandro A. and Yu, Yi-Kuo},
title = {PSI-BLAST pseudocounts and the minimum description length principle},
journal = {Nucleic acids research},
year = {2009},
volume = {37},
number = {3},
pages = {815--824},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1Rb9MwED4hNAkkhMYGLAyQJaBv7ZI4qeOHPUwVE7whbTxb5zhhiDat2lRi-_Xc2Um3DIQQr8k5UnzW3Xf25-8AZDqJx_digkbpdIppijXKAnVaFGjzqVZuqlRi5XBnG3oWGZMsB1TFSfP9ytMtu3ld-35rk5rrRn7kTinBK1qno3a5nJ-uFn5cdTMKhl6ICC1vIpQtxW3WS-sr_O7kgRJakJzyCp1Z0UuaannS4Prk249GF769DBOEEpkN8tngjtwdqPo743KPL51sN39Mdz61ne_D0w6TirPws8_gQdUcwOFZQ_X44lqMhGeJ-u33A3g06zvEHcLsy8Vn7lB1cSlWm2rrlr7xxEZg4wThSsGyJYvtQrhqF5sEN25pr8Sq3-N_Dl_PP17OPo27pgzjkqBWPs61Q6cQa61Kym7oCADqjFBRUmcOdZVbhVlmSy0t1S51LvPa2jShKGoVYZ9YvoAnyOT9pvWX_NwRiLgkmGi1kiXrb6GzikXkMa9iX0DbCN71c2xWQYTDhMNzacgpJjglgrc0_X81eNl7xrj53LDwEOVqQnj8xvvndnTn3gjUwHM7A5blHr6hpenlubsVGMGH4OPdkNRsUhObqZR82ppT5Wfan20ER_fsJNXshKP5E-_vro6dAacxipuSJosxawTJv5jNOtF3FjtoX_33fx3D43CixpSe1_CwXW-rN0HE8hfF2Dgu}
}
|
|||||
| Altschul, S.F., Gertz, E.M., Agarwala, R., Schäffer, A.A. and Yu, Y.-K. | PSI-BLAST pseudocounts and the minimum length principle [BibTeX] |
2009 | Nucleic acids research Vol. 37(3), pp. 815-824 |
article | |
BibTeX:
@article{altschul_psi-blast_2009-1,
author = {Altschul, Stephen F. and Gertz, E. M. and Agarwala, Richa and Schäffer, Alejandro A. and Yu, Yi-Kuo},
title = {PSI-BLAST pseudocounts and the minimum length principle},
journal = {Nucleic acids research},
year = {2009},
volume = {37},
number = {3},
pages = {815--824}
}
|
|||||
| Frieden, B.R. and Hawkins, R.J. | Quantifying system order for full and partial coarse graining | 2010 | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics Vol. 82(6), pp. 066117 |
article | URL |
| Abstract: We show that Fisher information I and its weighted versions effectively measure the order R of a large class of shift-invariant physical systems. This result follows from the assumption that R decreases under small perturbations caused by a coarse graining of the system. The form found for R is generally unitless, which allows the order for different phenomena to be compared objectively. The monotonic contraction properties of R and I in time imply that they are entropies, in addition to their usual status as information. This removes the need for data, and therefore an observer, in physical derivations based upon their use. Thus, this recognizes complementary scenarios to the participatory observer of Wheeler, where (now) physical phenomena can occur in the absence of an observer. Simple applications of the new order measure R are discussed.; We show that Fisher information I and its weighted versions effectively measure the order R of a large class of shift-invariant physical systems. This result follows from the assumption that R decreases under small perturbations caused by a coarse graining of the system. The form found for R is generally unitless, which allows the order for different phenomena to be compared objectively. The monotonic contraction properties of R and I in time imply that they are entropies, in addition to their usual status as information. This removes the need for data, and therefore an observer, in physical derivations based upon their use. Thus, this recognizes complementary scenarios to the participatory observer of Wheeler, where (now) physical phenomena can occur in the absence of an observer. Simple applications of the new order measure R are discussed. | |||||
BibTeX:
@article{frieden_quantifying_2010,
author = {Frieden, B. R. and Hawkins, Raymond J.},
title = {Quantifying system order for full and partial coarse graining},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
year = {2010},
volume = {82},
number = {6},
pages = {066117},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV3JTsMwEB0hBBISYoeGRfIBTtDixHacHFHVinMF58grt1LRgPh8xtlKSw_lkkPiOPKWN5558wzAkgHtr_wTjKeZZEwqKlTgVHm8gXPBcRN7ledm2bMND-sD-jFlj4EYOXFfo0GGn0FwiUMmOU9TUeWOTNq_MEMo4rVWao6LSIg2YWZtFUug1CHRTkgM-ZyvhaQKfsaH0LLvW9pJF4teZMv_pWVv1KwjOGhsUvJUT6Jj2HLTE9ituKFmfgpBZyNQikJCFKmVn0ml2EnQ4CXBf0_U1JJZmIRYjXnHvbIjb83ZE2fwOh69DJ_7zakLfRMHZ5TGRRwrrrRG68E6bxkzVFq0xBNnvNVJrhOWpsYZ6RNluKbe5tKn3GdCutSwc9hXgZ0_LassPtsDYnJJY6u8kZZyLoRGIyHRFq9KW2p9BPdt_xezWmWjqHYnlBVtzxRZUtQ9E8FFPURd2YC_aCuJCO7qMVs8Keb4WiGzVARMEEwU5XcZQW-lHMOKYzRHeQS3v0e7K1D5IdMQ9a0CIhHEmxQbNkLrQWCgvPxXK69gL-moM9ewXX58uptaLPIHaL39nQ}
}
|
|||||
| Ehrenfeucht, A., Kleijn, J., Koutny, M. and Rozenberg, G. | Reaction systems: A natural computing approach to the functioning of living cells [BibTeX] |
2012 | incollection | ||
BibTeX:
@incollection{ehrenfeucht_reaction_2012,
author = {Ehrenfeucht, Andrzej and Kleijn, Jetty and Koutny, Maciej and Rozenberg, Grzegorz},
title = {Reaction systems: A natural computing approach to the functioning of living cells},
year = {2012}
}
|
|||||
| Griffiths, P.E. and Gray, R.D. | Replicator II – Judgement Day | 1997 | Biology and Philosophy Vol. 12(4), pp. 471-492 |
article | URL |
| Abstract: The Developmental Systems approach to evolution is defended against the alternative ’extended replicator‘ approach of Sterelny, Smith and Dickison (1996). A precise definition is provided of the spatial and temporal boundaries of the ’life-cycle‘ that DST claims is the unit of evolution. Pacé Sterelny et al., the extended replicator theory is not a bulwark against excessive holism. Everything which DST claims is replicated in evolution can be shown to be an ’extended replicator‘ on Sterelny et al.‘s definition. Reasons are given for scepticism about the heuristic value claimed for the extended replicator concept. For every competitive, individualistic insight the replicator theorist has a cooperative, systematic blindspot.; The Developmental Systems approach to evolution is defended against the alternative 'extended replicator' approach of Sterelny, Smith and Dickison (1996). Aprecise definition is provided of the spatial and temporal boundaries of the 'life-cycle' that DST claims is the unit of evolution. PacB Sterelny et al., the extended replicator theory is not a bulwark against excessive holism. Everything which DST claims is replicated in evolution can be shown to be an 'extended replicator' on Sterelny et al.'s definition. Reasons are given for scepticism about the heuristic value claimed for the extended replicator concept. For every competitive, individualistic insight the replicator theorist has a cooperative, systematic blindspot.; The Developmental Systems approach to evolution is defended against the alternative 'extended replicator' approach of Sterelny, Smith and Dickison (1996). A precise definition is provided of the spatial and temporal boundaries of the 'life-cycle' that DST claims is the unit of evolution. Pacé Sterelny et al., the extended replicator theory is not a bulwark against excessive holism. Everything which DST claims is replicated in evolution can be shown to be an 'extended replicator' on Sterelny et al.'s definition. Reasons are given for scepticism about the heuristic value claimed for the extended replicator concept. For every competitive, individualistic insight the replicator theorist has a cooperative, systematic blindspot.[PUBLICATION ABSTRACT] | |||||
BibTeX:
@article{griffiths_replicator_1997,
author = {Griffiths, Paul E. and Gray, Russell D.},
title = {Replicator II – Judgement Day},
journal = {Biology and Philosophy},
year = {1997},
volume = {12},
number = {4},
pages = {471--492},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwjV1Lb9QwEB4hEKgSorRAGlpEDkicEsWx48cRtq1a4IB4CU6WN7YvrZbSzUrdW_8D_5BfwtjebLcLhz1acazEY898nsdnANpUdbmmE3zDxgFciJpY3nlD5biznalNI9qOsPFtzzbUS0_G5KwaApRRb69S86D1RGtMeK3CmR0NVVjhnz5_W2riYOsTt7cqqeRijdpn5f3b-DIUhMymK7HR_1qlaIGOt2FIQx4yT5bh6JuC-X8zszf-s8fwaAFNizdpLe3AHTfZhfvpssr5Lmx9HG49mD-Blwjco7vv52Vxelr8uf5dvJvZlEdTHJr5U_h6fPRldFIu7looLwhChDJcg-5N6xuHRxbLpAk070YR2wnPOXNOUMuE9CZsU-UVU1ZJ7xX3nDpiKX0GD03IyZ_0sXbPZnDP4wZyWTBqGU5WBg–qw-H8uT9KDV3hmY1jQVm1a8-Q8nF_VfySuxBUVtHW0E6RLWeEWZkYz1z0rSOB-3Y5ZANYtP2_FwjHJF4BlKU5LCXpKgvEmuHTkz2ouE5vFp71Ohpo-sYhycSIWmr-6s-h9eDfG7GUEpoRKRU4XCaaUIFTh4OuLo6lr0Do7D48TZ41oLhyYFs0m204GYPnAT9840_Yh-2IrNuzDM8gLv95cy9SNySfwHurADe}
}
|
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| Bergstrom, C.T. and Rosvall, M. | Response to commentaries on “The Transmission Sense of Information” [BibTeX] |
2011 | Biology & Philosophy Vol. 26(2), pp. 195-200 |
article | URL |
BibTeX:
@article{bergstrom_response_2011,
author = {Bergstrom, Carl T. and Rosvall, Martin},
title = {Response to commentaries on “The Transmission Sense of Information”},
journal = {Biology & Philosophy},
year = {2011},
volume = {26},
number = {2},
pages = {195--200},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1Lb9QwEB4hEKgSKrRAmvJQDnBBJErixLGP1UKpBAfUAuJmxXF8abW7dFOJ3vpD2j_XX8KMnaS7Sw_lGGXiVz7P-DHzDQDLkzRe0wnSCtNoxol-T9RZatpUG1x5VMy0wlR69WQb8vEkY3qcDBeUTm8vhb6VjDx9slgi6mLi-0RTRRg_PPo56mKy9p7dW8ZM8Gq417ythBXLtK6fiUm0mc3PFks3prfaKmeX9p_AEC8z-KOMl9Q3YfT_-mv_R3-fwma_ZI32PMa24F473YaHPonl-TZsfBuyIZw_g8-H3ue2jbpZhCU713TajUezaXR9cYmojJx5RHjROV101JLwzEZ9XBTh5Pri6jn82P_0fXIQ97ka4oa4zmPck6O6sFlZC97khcgKrQtpWKE5N5TNo82lZlbL2lpGLIHW8KIpysowaWuh2Qt4XJNP_7RzsX8mgAcWJ2AbkFEMcFgDePRLfv0oDr5M_OPW8JgsXIBa8rsL8L-7-RvzpNqByFiT85ZIEq0pKkRgkRlpdWbcblzrEN4Pv1zNPbuHuuFxphFXOOKKRlyxEN4QKJQPUB01g2KoFilrSx5C4ARINXSndbPyZgCSMicnKmcIRkdFGMI7j6ux_lwtcpUqIuorBcf9JFPdnw5LWJOjxDyobLHsDwNilvpATae1nerB4fswN5YqXBd3gv03HBtAsiG8XQb3KEsmVKZoBhgtdcoQsruITXrCeSJa6Hbv2ISXsOFP8Mnj7xXc707P2teeLvMvG5ZHPg}
}
|
|||||
| Frieden, B.R. | Science from Fisher information: a unification [BibTeX] |
2004 | book | URL | |
BibTeX:
@book{frieden_science_2004,
author = {Frieden, B. R.},
title = {Science from Fisher information: a unification},
publisher = {Cambridge University Press},
year = {2004},
edition = {2nd},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwdV1LawIxEB5qi1LooVZNbSvdP7DLbhLzOK8VoT320Jska3IURP8_TrJZ6hZ7HAaSYcg8mW8CwGhR5n98QthhYLiwlC2dUJRb4UQpDWZ22mi_E_3O9rW6sQdA7zoYGHsrKeUABljkXVhldMNcMK5ZwqdiKoFWnQiFNY9epvU7HVP_0pFf9TbzxXCzfoTbAEEYw43bP8EwDmk2xwm8J0PMAiYkaz8tz9Lm06DfKSzWH9_1Jg8HblNjZmuT-IrO4MGEgfb9KQLfdgTuPL4-R0JEIHg5gdGP_lqpzWfdkuOOLI4RnVUcTgQDUHy8uSjkM2SKuqpR3pfKM-6YtaVxjJkGcwRhra_mMLsuzst_jFe4bwdXQgfiLcm4aNV0Bswcf-Q}
}
|
|||||
| Godfrey-Smith, P. | Sender-Receiver Systems within and between Organisms | 2014 | Philosophy of Science Vol. 81(5), pp. 866-878 |
article | URL |
| Abstract: Drawing on models of communication due to Lewis and Skyrms, I contrast sender-receiver systems as they appear within and between organisms, and as they function in the bridging of space and time. Within the organism, memory can be seen as the sending of messages over time, communication between stages as opposed to spatial parts. Psychological memory and genetic memory are compared with respect to their relations to a sender-receiver model. Some puzzles about "genetic information" can be resolved by seeing the genome as a cell-level memory with no sender.; Drawing on models of communication due to Lewis and Skyrms, I contrast sender-receiver systems as they appear within and between organisms, and as they function in the bridging of space and time. Within the organism, memory can be seen as the sending of messages over time, communication between stages as opposed to spatial parts. Psychological memory and genetic memory are compared with respect to their relations to a sender-receiver model. Some puzzles about “genetic information” can be resolved by seeing the genome as a cell-level memory with no sender.; Drawing on models of communication due to Lewis and Skyrms, I contrast sender-receiver systems as they appear within and between organisms, and as they function in the bridging of space and time. Within the organism, memory can be seen as the sending of messages over time, communication between stages as opposed to spatial parts. Psychological memory and genetic memory are compared with respect to their relations to a sender-receiver model. Some puzzles about “genetic information” can be resolved by seeing the genome as a cell-level memory with no sender.; Drawing on models of communication due to Lewis and Skyrms, I contrast sender-receiver systems as they appear within and between organisms, and as they function in the bridging of space and time. Within the organism, memory can be seen as the sending of messages over time, communication between stages as opposed to spatial parts. Psychological memory and genetic memory are compared with respect to their relations to a sender-receiver model. Some puzzles about "genetic information" can be resolved by seeing the genome as a cell-level memory with no sender. | |||||
BibTeX:
@article{godfrey-smith_sender-receiver_2014,
author = {Godfrey-Smith, Peter},
title = {Sender-Receiver Systems within and between Organisms},
journal = {Philosophy of Science},
year = {2014},
volume = {81},
number = {5},
pages = {866--878},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwjV1LS8QwEB5EQQRR10ddH5iDBz10bZO0TY-yKoIexAd4K9kmC4IuateD_96ZpK27PtBj37Qz03zJzHwfgOC9KPzyT8jK3BDPh02MJIYxXRqRaamNLMvMOvL9iZVtYL8k9FV6lGYIkIliW2SCAvG6f9VmDWIV-T-viEPFpZrQEvKXTQ0-vv5wGllSK8hb9VWJ5MdByQ1AZ8vQKHM1hSdtNvqzX_57YfavL7YCSzUSZcfedTowY0ersHDVSBu8r0KnDvyKHdTs1IdrIG-c-FyIeNNSTQerOc8Zreg-jJgeGVYXfzHf6Fk9Vetwd3Z62z8Pa-mFsESAJkNOWS4EQ9KkguPkO1WDgUyTYYT2EibHqCflMpz7YbzHeam4RQPzhBudRJajaTZgUVOJ_mjsWvlMAHNDjCcb0BgX4McLYP4-vzxR5xd9v9lpNnuV6zfrvYwDNKwLxzDtZZvAxADx4pCniIIkkVxqrQc2IicSXEdKd2GvMW_x7Mk6CpdkV2nhP28X1pzV28PN7qBxgsI8PhaClNdjRHZxFza9T3xeQW2nuVJ4aHfKS4o6-qv2pvuTXtPewHECJUlGkvQ4Qe1C_J_T-jVlO1EVjLf-ePQ2LCCwk77sZgdmx69vdtcTTX4A9c0JNA}
}
|
|||||
| Godfrey-Smith, P. | Senders, receivers, and genetic information: comments on Bergstrom and Rosvall [BibTeX] |
2011 | Biology & Philosophy Vol. 26(2), pp. 177-181 |
article | |
BibTeX:
@article{godfrey-smith_senders_2011,
author = {Godfrey-Smith, Peter},
title = {Senders, receivers, and genetic information: comments on Bergstrom and Rosvall},
journal = {Biology & Philosophy},
year = {2011},
volume = {26},
number = {2},
pages = {177--181}
}
|
|||||
| Pande, V.S. | Simple theory of protein folding kinetics | 2010 | Physical Review Letters Vol. 105(19), pp. 198101 |
article | URL |
| Abstract: We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical properties seen in detailed simulations as well as to serve as a model to easily compare why these simulations suggest a different kinetic mechanism than previous simple models. Specifically, we find that non-native contacts play a key role in determining the mechanism, which can shift dramatically as the energetic strength of non-native interactions is changed. For proteinlike non-native interactions, our model finds that the native state is a kinetic hub, connecting the strength of relevant interactions directly to the nature of folding kinetics.; We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical properties seen in detailed simulations as well as to serve as a model to easily compare why these simulations suggest a different kinetic mechanism than previous simple models. Specifically, we find that non-native contacts play a key role in determining the mechanism, which can shift dramatically as the energetic strength of non-native interactions is changed. For proteinlike non-native interactions, our model finds that the native state is a kinetic hub, connecting the strength of relevant interactions directly to the nature of folding kinetics. | |||||
BibTeX:
@article{pande_simple_2010,
author = {Pande, Vijay S.},
title = {Simple theory of protein folding kinetics},
journal = {Physical Review Letters},
year = {2010},
volume = {105},
number = {19},
pages = {198101},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1JS8QwFH6IG4K4W-sCPejBQ2vSNJn2KKPDgB7EBbyVJk3Ay7hMFX–L8lMZ9xAj2kfabO9JXnfFwCWJiT-ohOYYhVXlPFcUYN6U1eG6zqtOMuUEY4zaWpnG8jPB_qUsBObGHmt3yzYxd5Rm2DQTB1-KxOCO_zIdauJaSq8JmY2DYF0Rgjh36v5ZJxaizRvASKvwx9NkzNDvVUY5yKP00_aM-kJav57evafm7cGKyP_NDr1E2odZvRgAxZcnqgabsLxzYOlE448pD96NNGVJXp4GEQ9f4wVXaDbaqmft-Cud37b7cej2xbiiqLFijH2EkUhiTQmr4lhHVlg6CY5T6sOk-inaSmtuyGFZsoYbnSWkyxT6C-qGlUV24blymblDxqH3qsDmDO4hHRgzVqAPRXA4n1xeZb3L7q-uD4uJkMHMUuemwDHzq3AWCSdHYjQoaXooiqTcZkZznOcOhhAK4o_VWdahnAyHrHyyfNzlC6uIayc6kt8xkvflyEEfmBbeWu9Kb4M4ciP9ORNOUxLUlpaMLvxQ5kom_cmhJ0vcowXRYrOlgjhcHqOtAJuF5PlWIudlvgl-hex7oim3dITNLv_bukeLLlcB4ec3IfZ5uVVH3i6yQ8-AwrI}
}
|
|||||
| Artiga, M. | Teleosemantics and Pushmi-Pullyu Representations | 2014 | Erkenntnis Vol. 79(S3), pp. 545-566 |
article | URL |
| Abstract: One of the main tenets of current teleosemantic theories is that simple representations are Pushmi-Pullyu states, i.e. they carry descriptive and imperative content at the same time. In the paper I present an argument that shows that if we add this claim to the core tenets of teleosemantics, then (1) it entails that, necessarily, all representations are Pushmi-Pullyu states and (2) it undermines one of the main motivations for the Pushmi-Pullyu account.; Issue Title: The first six articles belong to the Special Issue CAUSES AND (IN)DETERMINISM One of the main tenets of current teleosemantic theories is that simple representations are Pushmi-Pullyu states, i.e. they carry descriptive and imperative content at the same time. In the paper I present an argument that shows that if we add this claim to the core tenets of teleosemantics, then (1) it entails that, necessarily, all representations are Pushmi-Pullyu states and (2) it undermines one of the main motivations for the Pushmi-Pullyu account.[PUBLICATION ABSTRACT]; One of the main tenets of current teleosemantic theories is that simple representations are Pushmi-Pullyu states, i.e. they carry descriptive and imperative content at the same time. In the paper I present an argument that shows that if we add this claim to the core tenets of teleosemantics, then (1) it entails that, necessarily, all representations are Pushmi-Pullyu states and (2) it undermines one of the main motivations for the Pushmi-Pullyu account.; One of the main tenets of current teleosemantic theories is that simple representations are Pushmi-Pullyu states, i.e. they carry descriptive and imperative content at the same time. In the paper I present an argument that shows that if we add this claim to the core tenets of teleosemantics, then (1) it entails that, necessarily, all representations are Pushmi-Pullyu states and (2) it undermines one of the main motivations for the Pushmi-Pullyu account. | |||||
BibTeX:
@article{artiga_teleosemantics_2014,
author = {Artiga, Marc},
title = {Teleosemantics and Pushmi-Pullyu Representations},
journal = {Erkenntnis},
year = {2014},
volume = {79},
number = {S3},
pages = {545--566},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1Lb9swDCaKDRgKFOvbS9sBPqy32bAt25KORdaiwHYI2qzYTZBleSvWPBYnh_z7kn41SHLIjrJoQ_JHiqREUgAs8gNvbU0o0A_SZE-gQxJkVCQrMBkqT615IRKztrMNUbeTMf7rtweU1bq9kvqW0pUpIfPQRuAepZmjqiIef3h86tbixuWinB2PvJ_2XHPbFzYXZSofaibTRblyTLpVQVXK6O4Q2iSZNgilO5l-y53fDNL-j0kewcfGTnVvasY6hj07PoH9QXvxwfIUgiFqrElpR4jNsyldPc7dwaL8M3r2BujXLhfuQxVl2yQ3jcsz-Hl3O-zfe839C97vMEavUsRRkWpUWIIKgwWhtTKIcmkF01kmjC4yyQvycXkcW2mCMLeFiKyxeYJSnUt2Dgea4vRpGGg55w68L1CorEOKzsG_5sCHX_LHN3H_vV83j9umX1ZJZ_6_uYNYVjLppT7_BC6yfihSYxhHWzDOtE6kZhwHxZmxzAY9cAhGRQI6n2mjWIpWV5xIiT0tsip_eVEsEkLG-JkQe2qg1bSu8aGSiBOvJj342kLT9VWoKLScmGpQUASPmuZFD643yJEwbt7hUrGKtgdfVrmooyUXlVVV0UhYcC7hLmT9ppw7lTGYX-w4hEvYp8d1FNIVvJvPFvZzXYzyFfIjELk}
}
|
|||||
| Artiga, M. | Teleosemantics, Infotel-semantics and Circularity | 2014 | International Journal of Philosophical Studies Vol. 22(4), pp. 583-603 |
article | URL |
| Abstract: Peter Godfrey-Smith and Nicholas Shea have argued that standard versions of teleosemantics render explanations of successful behavior by appealing to true beliefs circular and, consequently, non-explanatory. As an alternative, Shea has recently suggested an original teleosemantic account (that he calls 'Infotel-semantics'), which is supposed to be immune to the problem of circularity. The paper argues that the standard version of teleosemantics has a satisfactory reply to the circularity objection and that, in any case, Infotel-semantics is not better off than standard teleosemantics.; Peter Godfrey-Smith and Nicholas Shea have argued that standard versions of teleosemantics render explanations of successful behavior by appealing to true beliefs circular and, consequently, non-explanatory. As an alternative, Shea has recently suggested an original teleosemantic account (that he calls 'Infotel-semantics'), which is supposed to be immune to the problem of circularity. The paper argues that the standard version of teleosemantics has a satisfactory reply to the circularity objection and that, in any case, Infotel-semantics is not better off than standard teleosemantics.; Peter Godfrey-Smith and Nicholas Shea have argued that standard versions of teleosemantics render explanations of successful behavior by appealing to true beliefs circular and, consequently, non-explanatory. As an alternative, Shea has recently suggested an original teleosemantic account (that he calls 'Infotel-semantics'), which is supposed to be immune to the problem of circularity. The paper argues that the standard version of teleosemantics has a satisfactory reply to the circularity objection and that, in any case, Infotel-semantics is not better off than standard teleosemantics. | |||||
BibTeX:
@article{artiga_teleosemantics_2014-1,
author = {Artiga, Marc},
title = {Teleosemantics, Infotel-semantics and Circularity},
journal = {International Journal of Philosophical Studies},
year = {2014},
volume = {22},
number = {4},
pages = {583--603},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1Lq9QwFD6IglwQ9fqo4wO6cGlr2zSPWcroMKALFyO4KydNAhfG123vwn_vOWlT78gV5S7TNG2TnOR8p_nyBUA0ZVX8MScgVjVWuBbetYgGXbW2KpgmoBWhkXj8ZxuSKgSTLDmiDpNsRJy5eaijHRI_7jVhcM24mGlabUnudxb_FJoZXvvtbpmYm3nBmQoUXCLtpPvLQ4481ZGO6TEa5e0jF8OVjis6qe09SKypRE5ZVqx_76m_grx9zcrfh7szmM3fTNZ3Cjf81wdw8jGdjvDzIdR7cmvfBv-FOvCsH17lvMo1-kOxXMrp3fnm7DzyYSkkeASftu_2m10xn9JQ9BQ86qL3jVdGBm2k7G0InlGBDNYp1yjtDEoMqNe65thMW4Ota2oCXdaaWvgexWO4g8zm55cSvnYZ3Ao09HzG7jCjNszg9uf1h7dm934zJU9Tshzi1rTyx5hRJ8eRW6hSP4G8lUJ5si0KgHwbkOJw2QelnLJVg611KyhS53bfJ12Prk5yqXOjdtyo3dSoK9CXLaAb4_-UMB1-8o-SWTKWzh0OnZAc90q6g3Im21m-gCZEAmxGr-DlZWNa8qOckCBQqOMS9Arq_7ltM6u9s8rB-PTaFXkGJ5yK7EfzHG6O5xf-xaRe-QsDNyDr}
}
|
|||||
| Macdonald, G. and Papineau, D. | Teleosemantics: new philosophical essays [BibTeX] |
2006 | book | ||
BibTeX:
@book{macdonald_teleosemantics:_2006,
author = {Macdonald, Graham and Papineau, David},
title = {Teleosemantics: new philosophical essays},
publisher = {Oxford University Press},
year = {2006}
}
|
|||||
| Abel, D.L. | The biosemiosis of prescriptive information | 2009 | Semiotica Vol. 2009(174), pp. 1-19 |
article | |
| Abstract: Exactly how do the sign/symbol/token systems of endo- and exo-biosemiosis differ from those of cognitive semiosis? Do the biological messages that integrate metabolism have conceptual meaning? Semantic information has two subsets: Descriptive and Prescriptive. Prescriptive information instructs or directly produces nontrivial function. In cognitive semiosis, prescriptive information requires anticipation and "choice with intent" at bona fide decision nodes. Prescriptive information either tells us what choices to make, or it is a recordation of wise choices already made. Symbol systems allow recordation of deliberate choices and the transmission of linear digital prescriptive information. Formal symbol selection can be instantiated into physicality using physical symbol vehicles (tokens). Material symbol systems (MSS) formally assign representational meaning to physical objects. Even verbal semiosis instantiates meaning into physical sound waves using an MSS. Formal function can also be incorporated into physicality through the use of dynamically-inert (dynamically-incoherent or -decoupled) configurable switch-settings in conceptual circuits. This article examines the degree to which biosemiosis conforms to the essential formal criteria of prescriptive semiosis and cybernetic management. | |||||
BibTeX:
@article{abel_biosemiosis_2009,
author = {Abel, David L.},
title = {The biosemiosis of prescriptive information},
journal = {Semiotica},
year = {2009},
volume = {2009},
number = {174},
pages = {1--19}
}
|
|||||
| Abel, D.L. | The biosemiosis of prescriptive information | 2009 | Semiotica Vol. 2009(174), pp. 1-19 |
article | |
| Abstract: Exactly how do the sign/symbol/token systems of endo- and exo-biosemiosis differ from those of cognitive semiosis? Do the biological messages that integrate metabolism have conceptual meaning? Semantic information has two subsets: Descriptive and Prescriptive. Prescriptive information instructs or directly produces nontrivial function. In cognitive semiosis, prescriptive information requires anticipation and "choice with intent" at bona fide decision nodes. Prescriptive information either tells us what choices to make, or it is a recordation of wise choices already made. Symbol systems allow recordation of deliberate choices and the transmission of linear digital prescriptive information. Formal symbol selection can be instantiated into physicality using physical symbol vehicles (tokens). Material symbol systems (MSS) formally assign representational meaning to physical objects. Even verbal semiosis instantiates meaning into physical sound waves using an MSS. Formal function can also be incorporated into physicality through the use of dynamically-inert (dynamically-incoherent or -decoupled) configurable switch-settings in conceptual circuits. This article examines the degree to which biosemiosis conforms to the essential formal criteria of prescriptive semiosis and cybernetic management. | |||||
BibTeX:
@article{abel_biosemiosis_2009,
author = {Abel, David L.},
title = {The biosemiosis of prescriptive information},
journal = {Semiotica},
year = {2009},
volume = {2009},
number = {174},
pages = {1--19}
}
|
|||||
| Beni, M.D. | The Code Model of Biosemiotics and the Fate of the Structuralist Theory of Mental Representation [BibTeX] |
2016 | Biosemiotics | article | |
BibTeX:
@article{beni_code_2016,
author = {Beni, Majid D.},
title = {The Code Model of Biosemiotics and the Fate of the Structuralist Theory of Mental Representation},
journal = {Biosemiotics},
year = {2016}
}
|
|||||
| Sella, G. and Ardell, D.H. | The Coevolution of Genes and Genetic Codes: Crick’s Frozen Accident Revisited [BibTeX] |
2006 | Journal of Molecular Evolution Vol. 63(3), pp. 297-313 |
article | |
BibTeX:
@article{sella_coevolution_2006,
author = {Sella, Guy and Ardell, David H.},
title = {The Coevolution of Genes and Genetic Codes: Crick’s Frozen Accident Revisited},
journal = {Journal of Molecular Evolution},
year = {2006},
volume = {63},
number = {3},
pages = {297--313}
}
|
|||||
| Wang, Y. | The cognitive informatics theory and mathematical models of visual information processing in the brain [BibTeX] |
2009 | International Journal of Cognitive Informatics and Natural Intelligence Vol. 3(3), pp. 1-11 |
article | |
BibTeX:
@article{wang_cognitive_2009,
author = {Wang, Yingxu},
title = {The cognitive informatics theory and mathematical models of visual information processing in the brain},
journal = {International Journal of Cognitive Informatics and Natural Intelligence},
year = {2009},
volume = {3},
number = {3},
pages = {1--11}
}
|
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| Di Giulio, M. | The Early Phases of Genetic Code Origin: Conjectures on the Evolution of Coded Catalysis | 2003 | Origins of Life and Evolution of the Biosphere Vol. 33(4), pp. 479-489 |
article | URL |
| Abstract: A review of the most significant contributions on the early phases of genetic code origin is presented. After stressing the importance of the key intermediary role played in protein synthesis, by peptidyl-tRNA, which is attributed with a primary function in ancestral catalysis, the general lines leading to the codification of the first amino acids in the genetic code are discussed. This is achieved by means of a model of protoribosome evolution which sees protoribosome as the central organiser of ancestral biosynthesis and the mediator of the encounter between compounds (metabolite-pre-tRNAs) and catalysts (peptidyl-pre-tRNAs). The encounter between peptidyl-pre-tRNA catalysts in protoribosome is favoured by metabolic pre-mRNAs and later resulted (given the high temperature at which this evolution is supposed to have taken place) in the evolution of mRNAs with codons of the type GNS. These mRNAs codified only for those amino acids that the coevolution theory of genetic code origin sees as the precursors of all other amino acids. Some aspects of the model here discussed might be rendered real by the transfer-messenger RNA molecule (tmRNA) which is here considered a molecular fossil of ancestral protein synthesis.; A review of the most significant contributions on the early phases of genetic code origin is presented. After stressing the importance of the key intermediary role played in protein synthesis, by peptidyl-tRNA, which is attributed with a primary function in ancestral catalysis, the general lines leading to the codification of the first amino acids in the genetic code are discussed. This is achieved by means of a model of protoribosome evolution which sees protoribosome as the central organiser of ancestral biosynthesis and the mediator of the encounter between compounds (metabolite-pre-tRNAs) and catalysts (peptidyl-pre-tRNAs). The encounter between peptidyl-pre-tRNA catalysts in protoribosome is favoured by metabolic pre-mRNAs and later resulted ( given the high temperature at which this evolution is supposed to have taken place) in the evolution of mRNAs with codons of the type GNS. These mRNAs codified only for those amino acids that the coevolution theory of genetic code origin sees as the precursors of all other amino acids. Some aspects of the model here discussed might be rendered real by the transfer-messenger RNA molecule ( tmRNA) which is here considered a molecular fossil of ancestral protein synthesis.; A review of the most significant contributions on the early phases of genetic code origin is presented. After stressing the importance of the key intermediary role played in protein synthesis, by peptidyl-tRNA, which is attributed with a primary function in ancestral catalysis, the general lines leading to the codification of the first amino acids in the genetic code are discussed. This is achieved by means of a model of protoribosome evolution which sees protoribosome as the central organiser of ancestral biosynthesis and the mediator of the encounter between compounds (metabolite-pre-tRNAs) and catalysts (peptidyl-pre-tRNAs). The encounter between peptidyl-pre-tRNA catalysts in protoribosome is favoured by metabolic pre-mRNAs and later resulted (given the high temperature at which this evolution is supposed to have taken place) in the evolution of mRNAs with codons of the type GNS. These mRNAs codified only for those amino acids that the coevolution theory of genetic code origin sees as the precursors of all other amino acids. Some aspects of the model here discussed might be rendered real by the transfer-messenger RNA molecule (tmRNA) which is here considered a molecular fossil of ancestral protein synthesis.[PUBLICATION ABSTRACT]; A review of the most significant contributions on the early phases of genetic code origin is presented. After stressing the importance of the key intermediary role played in protein synthesis, by peptidyl-tRNA, which is attributed with a primary function in ancestral catalysis, the general lines leading to the codification of the first amino acids in the genetic code are discussed. This is achieved by means of a model of protoribosome evolution which sees protoribosome as the central organiser of ancestral biosynthesis and the mediator of the encounter between compounds (metabolite-pre-tRNAs) and catalysts (peptidyl-pre-tRNAs). The encounter between peptidyl-pre-tRNA catalysts in protoribosome is favoured by metabolic pre-mRNAs and later resulted (given the high temperature at which this evolution is supposed to have taken place) in the evolution of mRNAs with codons of the type GNS. These mRNAs codified only for those amino acids that the coevolution theory of genetic code origin sees as the precursors of all other amino acids. Some aspects of the model here discussed might be rendered real by the transfer-messenger RNA molecule (tmRNA) which is here considered a molecular fossil of ancestral protein synthesis. | |||||
BibTeX:
@article{di_giulio_early_2003,
author = {Di Giulio, Massimo},
title = {The Early Phases of Genetic Code Origin: Conjectures on the Evolution of Coded Catalysis},
journal = {Origins of Life and Evolution of the Biosphere},
year = {2003},
volume = {33},
number = {4},
pages = {479--489},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwjV1Lb9QwEB4hEFAJAV1oujwkHxDiksV2nBe3KlBVAgnES71ZWT9UQdldSIrov2fGSXajbQ97Wytjy9l89jw88xkgkTMeb-0JTs1zK2xpysRk1nBhVOpqkdY25cqFIrVRZBv4OpKx-DkbDijDvj2m5kG05eQx8IQK-FBREcI_f_m-Id3taRlFVqKLpMotap9R_-vsSyIPNcvVRTM6JL1WPQVVdPwAhnzkIQVlfS69qZy_mqK98ys-hPu9jcqOOlDtww23mMDhUUNR8-WvS_aShd9dUKSZwO3uQsvLCdythvvjHsEpIpAF_mT26Qx1ZcOWnhHLNY7KqqV17GO4lOsNNhY_uqMMlFmwlvr97ZcEdSJhyyoKNBF_ymP4dvzua3US9_c4xCuh0iIusmxeC-fwC9W-KLzxc1v4LE2TVCAsMi-NMj4Txtna5iYXLs_T1FhXWJ7U0icHcK-mfP9FG-oCbQS3PC5OF5HCjPD_j-DOafnhbXHyvuqa-0Nz1oTitdnvNkJUhLUdZ7P8EBjq7tokvFC1KZWby7IQvlbeSe69srKcQjRAQtvzc42mp6S65FLQk4AQveoYQch_4koU-RRedJBZP5G6kZprdEQlzyXax7r91-IAW2J0eCpVwqfwesDCZnCBk6TrQpXuP7xGKxd3TqlX1k_h1ZUelHDYd0sSrQZxnN0YvGtxsvPRakNPO3gQUxC7iFU9hzxxJ7RPdp_FU9jbJEQ-g5vtnwv3vCPB_A9chjnW}
}
|
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| Wolynes, P. | The Energy Landscape Theory of Protein Folding [BibTeX] |
2008 | inproceedings | URL | |
BibTeX:
@inproceedings{wolynes_energy_2008,
author = {Wolynes, Peter},
title = {The Energy Landscape Theory of Protein Folding},
year = {2008},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1NS8NAEB2UgghCLda1rcLiPWuyTbrm5KE2FOxB0IO3stmPY2tp_j_u7GZTsdCDkMsSApNkeLM7894MwJSzNPmDCUKbTGlji9SqWZEJm2rhjs9YBpOq9M36f2W2u_xb-7cjSHrk1luFSfMn7OyF7eVevncJDpHCYms7UeMceplwruzcW3xURyjrQ0fVh0gbiJSRro58ULofU6r_adI1DA8SPvreBacBnJnNDTDnFHTh1X50hRpfZD_RIM-nW4sP4PBLWoWS1BAeq8XnfJlEM9ayxsyIavbraAS_hSuJLPlN49V0mkDPOpc2BMMMcV-BwMVXuXp9Xr7Nw3IQl2zvJV9s1xAX1fwLJDMm7oBOc6mUgwVVS57bTNaZzK3bZNii5FoZOYLJCZvGJ-9O4DKwMbi77ltrH0J_xB851bNa}
}
|
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| English, S., Pen, I., Shea, N. and Uller, T. | The Information Value of Non-Genetic Inheritance in Plants and Animals | 2015 | PLOS ONE Vol. 10(1), pp. e0116996 |
article | URL |
| Abstract: Parents influence the development of their offspring in many ways beyond the transmission of DNA. This includes transfer of epigenetic states, nutrients, antibodies and hormones, and behavioural interactions after birth. While the evolutionary consequences of such non-genetic inheritance are increasingly well understood, less is known about how inheritance mechanisms evolve. Here, we present a simple but versatile model to explore the adaptive evolution of non-genetic inheritance. Our model is based on a switch mechanism that produces alternative phenotypes in response to different inputs, including genes and non-genetic factors transmitted from parents and the environment experienced during development. This framework shows how genetic and non-genetic inheritance mechanisms and environmental conditions can act as cues by carrying correlational information about future selective conditions. Differential use of these cues is manifested as different degrees of genetic, parental or environmental morph determination. We use this framework to evaluate the conditions favouring non-genetic inheritance, as opposed to genetic determination of phenotype or within-generation plasticity, by applying it to two putative examples of adaptive non-genetic inheritance: maternal effects on seed germination in plants and transgenerational phase shift in desert locusts. Our simulation models show how the adaptive value of non-genetic inheritance depends on its mechanism, the pace of environmental change, and life history characteristics.; Parents influence the development of their offspring in many ways beyond the transmission of DNA. This includes transfer of epigenetic states, nutrients, antibodies and hormones, and behavioural interactions after birth. While the evolutionary consequences of such non-genetic inheritance are increasingly well understood, less is known about how inheritance mechanisms evolve. Here, we present a simple but versatile model to explore the adaptive evolution of non-genetic inheritance. Our model is based on a switch mechanism that produces alternative phenotypes in response to different inputs, including genes and non-genetic factors transmitted from parents and the environment experienced during development. This framework shows how genetic and non-genetic inheritance mechanisms and environmental conditions can act as cues by carrying correlational information about future selective conditions. Differential use of these cues is manifested as different degrees of genetic, parental or environmental morph determination. We use this framework to evaluate the conditions favouring non-genetic inheritance, as opposed to genetic determination of phenotype or within-generation plasticity, by applying it to two putative examples of adaptive non-genetic inheritance: maternal effects on seed germination in plants and transgenerational phase shift in desert locusts. Our simulation models show how the adaptive value of non-genetic inheritance depends on its mechanism, the pace of environmental change, and life history characteristics. | |||||
BibTeX:
@article{english_information_2015,
author = {English, S. and Pen, I. and Shea, N. and Uller, T.},
title = {The Information Value of Non-Genetic Inheritance in Plants and Animals},
journal = {PLOS ONE},
year = {2015},
volume = {10},
number = {1},
pages = {e0116996},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw3V3Pa9swFBZjG2MwRrMfbroOdNhhY8jYViLLhx1G2lLYDoMmsFuQJRkCSZwu7v_f9yRZcboNdt4tiuXY0Sc9fe9J7xMhvEgz9sAmSFVzI1QjRKVrYWAO4kU9UbWCTlDXXD2IbPcH7B2–1-AD3KoDluU83aBAXD0GdyFWYtQAfP-OpcvgPvI1247jBduXW3Uej8krT_W7c3n9rD-HlJ_XeAUSKoyB_vq88hMGwM3YOtDh0MnOhL4RZ-BOG_rlTqKPfi8y9R6SwnEj4ki40emNPuty3i7aHG9p_Jn18ZW322g2ZFy8bzIDvNR3CUYL6EK-sasdPfFbtniBgUDJrnsQzN-2gXDLfA8qv6mI54RycVTzPW52_-RZThGMT8hL4MrQL96CEfkkd2-IqNgbPf0Y1AE__SaXAGmdIApdZjStqEDTOkAU_hMPaYUMKUB0zdkcXU5n12zcAAG00AbMia5lRr86UY3MEx4YbiagsG0UK6BhxouKomCbKXJdKFQbE5ZYad8KoGll8Lwt-SFwkSJbecSKk1CnjTwOJsg00jgHyfk2c_q-4W8_jbzxVFfTPcu6y-97RJoYTc2mEjLU0JLWeXSTIpcV-C8VrnS8F7W6MYoY3PbjAnrW36585IpS7duWoKr6Zt2uYNOuwx9YkwSD0-s3WM4Jqcer3hFZOBAgAeej8mHIYKxghNcAlbL8aCPCfxC_i_VZkEPH3UgurO_vs878hxHgY_AnZPH3a87-97rd94DERmLKg}
}
|
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| Dill, K.A., Ozkan, S.B., Shell, M.S. and Weikl, T.R. | The protein folding problem | 2008 | Vol. 37, pp. 289-316 |
inproceedings | URL |
| Abstract: The "protein folding problem" consists of three closely related puzzles: (a)What is the folding code? (b) What is the folding mechanism? (c) Can we predict the native structure of a protein from its amino acid sequence? Once regarded as a grand challenge, protein folding has seen great progress in recent years. Now, foldable proteins and nonbiological polymers are being designed routinely and moving toward successful applications. The structures of small proteins are now often well predicted by computer methods. And, there is now a testable explanation for how a protein can fold so quickly: A protein solves its large global optimization problem as a series of smaller local optimization problems, growing and assembling the native structure from peptide fragments, local structures first.; The "protein folding problem" consists of three closely related puzzles: (a) What is the folding code? (b) What is the folding mechanism? (c) Can we predict the native structure of a protein from its amino acid sequence? Once regarded as a grand challenge, protein folding has seen great progress in recent years. Now, foldable proteins and nonbiological polymers are being designed routinely and moving toward successful applications. The structures of small proteins are now often well predicted by computer methods. And, there is now a testable explanation for how a protein can fold so quickly: A protein solves its large global optimization problem as a series of smaller local optimization problems, growing and assembling the native structure from peptide fragments, local structures first. | |||||
BibTeX:
@inproceedings{dill_protein_2008,
author = {Dill, Ken A. and Ozkan, S. B. and Shell, M. S. and Weikl, Thomas R.},
title = {The protein folding problem},
publisher = {ANNUAL REVIEWS},
year = {2008},
volume = {37},
pages = {289--316},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV1LT9wwEB4hShFSxaNACLTSHlqpl40cP2L7iJaukMqhqorEzfIjkbhsgQ2I_vt64k1Ylh5Qe7RiR_LM2PPwfDMAjBZkvHIn1Dyo0CjihFfM0yBpaBgLXunS6qqDWi1Ftocky5UH_eXuLO76F_r-BZMF0VRinERgqXBEkwvdIblOf_R3sqhkwhlphl1n6NUmfHntD58prEFLbSBo5H7-V3XVqabpDvTx-T4lZXinfkLSv0zZ_oct78L2wnodnSZx24O1evYe3qZ-lr_34SQK3eg7Vn64no2m6V0Lx9iy5gAup19_Ts7Hi-4LY0uxx62vS-G00t7XTbDRuvXEOtqUlZfBV5wwLnmwhAYlsc-nq3jwmliuXfRynFPsEN5ZzNKftR2aL2TwpolHqs5QzWWRShlsXumLM3X-bZKGe_2wmHeQs-K2zSIHuxM5rgp5BCOBwRqhrYuOadSr0hIehdB5J8pGN1rmoHtumZtUr8M8x14_mAUdDZMm0dEkOuaQJfY-rVQi3oCK5fA58Xv4Qs2cGmK4iu5ryXh0ck372OZwtDIPq83y6INXOXxalpRhAqokoUq03NB-zaF8zbTJooA7Fi5oj_9jzyewlTJgMK70Adbbu_v6YypJ-Qf0wxZd}
}
|
|||||
| Dill, K.A., Ozkan, S.B., Weikl, T.R., Chodera, J.D. and Voelz, V.A. | The protein folding problem: when will it be solved? | 2007 | Current Opinion in Structural Biology Vol. 17(3), pp. 342-346 |
article | URL |
| Abstract: The protein folding problem can be viewed as three different problems: defining the thermodynamic folding code; devising a good computational structure prediction algorithm; and answering Levinthal's question regarding the kinetic mechanism of how proteins can fold so quickly. Once regarded as a grand challenge, protein folding has seen much progress in recent years. Folding codes are now being used to successfully design proteins and non-biological foldable polymers; aided by the Critical Assessment of Techniques for Structure Prediction (CASP) competition, protein structure prediction has now become quite good. Even the once-challenging Levinthal puzzle now seems to have an answer–a protein can avoid searching irrelevant conformations and fold quickly by making local independent decisions first, followed by non-local global decisions later. | |||||
BibTeX:
@article{dill_protein_2007,
author = {Dill, Ken A. and Ozkan, S. B. and Weikl, Thomas R. and Chodera, John D. and Voelz, Vincent A.},
title = {The protein folding problem: when will it be solved?},
journal = {Current Opinion in Structural Biology},
year = {2007},
volume = {17},
number = {3},
pages = {342--346},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1LT8MwDI7QJAQXHuM1HlLOSGVdmicXBIOKOyBxi9IsFUWoTGOA-PfETbppCDjs0EubNmqc2q79-TNCGTlLkx86QTIjRGGoNFwZIcsiKzllzClrFUuNXIxsh9KYCLKMliBo-EZ3xzP9uLb9cVX17yCeRWn66LcwUNSAVmZcAsgvv76a6WagvQzseyqB0W2es0F8vRVV5DRsEhR_Waqouhe80MYa5ZuohUC1KJRZanpePP8LSnv5t9xCG9FxxZdh3DZacXUXrYZWll9dtDZsO8ftIOr3Hm4IIKoalyG9hWPnmnP8-eRq7D30F1xNceGw3_wfbnSxix7ym_vhbRK7MyS2gawOSDpSUJc74sAbl9oMWt5Qa4wyWaoKr7mYAzJ3Yf1BufOWj5VMOJ4Zwr3XtIc69WvtDhC2xBpBpOWQFPX_X1KUUhEhHLTu9E_qodNWEnocSDh0i0571l5s0ExT6IDQ6yHaykovrKr2RuK_2_ZBrhq-6-nEWD3gnABVAPFXgqjncwsmiHe1D5eb6githwgxBHKOUWc6eXcngQbyG9qG7xA}
}
|
|||||
| Godfrey-Smith, P. | The role of information and replication in selection processes | 2001 | Behavioral and Brain Sciences Vol. 24(3), pp. 538-538 |
article | URL |
| Abstract: Hull et al. argue that information and replication are both essential ingredients in any selection process, But both information and replication are found in only some selection processes, and should not be included in abstract descriptions of selection intended to help researchers discover and describe selection processes in new domains.; Hull et al. argue that information and replication are both essential ingredients in any selection process. But both information and replication are found in only some selection processes, and should not be included in abstract descriptions of selection intented to help researchers deiscover describe selection processes in new domains. | |||||
BibTeX:
@article{godfrey-smith_role_2001,
author = {Godfrey-Smith, Peter},
title = {The role of information and replication in selection processes},
journal = {Behavioral and Brain Sciences},
year = {2001},
volume = {24},
number = {3},
pages = {538--538},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1NT9wwEB2VVkVIiBZYwvIh-VBxyyp2nMS5VNpuu1qpHEHiZjmJc6LLsglS-fedsZOwYjnQW6xYVjIej2fsN28AYjGJwlc2wYqqzCL0NWxZJBYtYCpLzguVlDwzyhVz2DjZhr5oXydPlH6fwOSpgws6BihbD01KRHJHNwboWmDsvoP7MwXts-kL0kO6mmkOyUidN2kUti0xcYaWD6un5s2tyG078y_Qg2t7uMlwB_2SJb8Nx_7v3_kKB51fyqZekQ7hg10ewfF0iTH5n2d2xRxS1B3BH8HnH_3T3mA_n4_hO6ocI7Qie6hZR8hK087MsmJrO1yU4zvWuPI71Fj5TAXbjOB2_utmtgi78gxhyWMVhdLEhlsMUEwhDI8MrnxZ0y1jin6AyLmN05ro3vOstrGwBUZyiSINiA12RNNyAvuGYPzL1qX7VQF8qlE6NqB9MEBRB7B7l1__VIvfM9887JuTxuWkTR7bAGfZLdkwnWSnwFRVFUrlsjCmlkkk8NuUTY0UprRZpaoxfBukr_sJ2Zb8GE5ILzRJiyZHZ-iKJnHOxzDqNUVX9_dayVzyXAoc16uNXnmaEC10I7QjX5Wu4CTX7d92DMGrbiiqLI2kxAE21W147ymN0O2j0hUZfhh_T7dZx_BOzAbt2fv–Rz2PMKOzpgu4GO7frKXnp7yHzt4HnM}
}
|
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| Bergstrom, C.T. and Rosvall, M. | The transmission sense of information | 2011 | Biology & Philosophy Vol. 26(2), pp. 159-176 |
article | URL |
| Abstract: Biologists rely heavily on the language of information, coding, and transmission that is commonplace in the field of information theory developed by Claude Shannon, but there is open debate about whether such language is anything more than facile metaphor. Philosophers of biology have argued that when biologists talk about information in genes and in evolution, they are not talking about the sort of information that Shannon's theory addresses. First, philosophers have suggested that Shannon's theory is only useful for developing a shallow notion of correlation, the so-called "causal sense" of information. Second, they typically argue that in genetics and evolutionary biology, information language is used in a "semantic sense," whereas semantics are deliberately omitted from Shannon's theory. Neither critique is well-founded. Here we propose an alternative to the causal and semantic senses of information: a transmission sense of information, in which an object X conveys information if the function of X is to reduce, by virtue of its sequence properties, uncertainty on the part of an agent who observes X. The transmission sense not only captures much of what biologists intend when they talk about information in genes, but also brings Shannon's theory back to the fore. By taking the viewpoint of a communications engineer and focusing on the decision problem of how information is to be packaged for transport, this approach resolves several problems that have plagued the information concept in biology, and highlights a number of important features of the way that information is encoded, stored, and transmitted as genetic sequence. Keywords Information * Evolution * Shannon theory * Natural selection * Entropy * Mutual information;Biologists rely heavily on the language of information, coding, and transmission that is commonplace in the field of information theory developed by Claude Shannon, but there is open debate about whether such language is anything more than facile metaphor. Philosophers of biology have argued that when biologists talk about information in genes and in evolution, they are not talking about the sort of information that Shannon’s theory addresses. First, philosophers have suggested that Shannon’s theory is only useful for developing a shallow notion of correlation, the so-called “causal sense” of information. Second, they typically argue that in genetics and evolutionary biology, information language is used in a “semantic sense,” whereas semantics are deliberately omitted from Shannon’s theory. Neither critique is well-founded. Here we propose an alternative to the causal and semantic senses of information: a transmission sense of information, in which an object X conveys information if the function of X is to reduce, by virtue of its sequence properties, uncertainty on the part of an agent who observes X. The transmission sense not only captures much of what biologists intend when they talk about information in genes, but also brings Shannon’s theory back to the fore. By taking the viewpoint of a communications engineer and focusing on the decision problem of how information is to be packaged for transport, this approach resolves several problems that have plagued the information concept in biology, and highlights a number of important features of the way that information is encoded, stored, and transmitted as genetic sequence.;Biologists rely heavily on the language of information, coding, and transmission that is commonplace in the field of information theory developed by Claude Shannon, but there is open debate about whether such language is anything more than facile metaphor. Philosophers of biology have argued that when biologists talk about information in genes and in evolution, they are not talking about the sort of information that Shannon’s theory addresses. First, philosophers have suggested that Shannon’s theory is only useful for developing a shallow notion of correlation, the so-called “causal sense” of information. Second, they typically argue that in genetics and evolutionary biology, information language is used in a “semantic sense,” whereas semantics are deliberately omitted from Shannon’s theory. Neither critique is well-founded. Here we propose an alternative to the causal and semantic senses of information: atransmission sense of information, in which an object X conveys information if the function of X is to reduce, by virtue of its sequence properties, uncertainty on the part of an agent who observes X. The transmission sense not only captures much of what biologists intend when they talk about information in genes, but also brings Shannon’s theory back to the fore. By taking the viewpoint of a communications engineer and focusing on the decision problem of how information is to be packaged for transport, this approach resolves several problems that have plagued the information concept in biology, and highlights a number of important features of the way that information is encoded, stored, and transmitted as genetic sequence.; Biologists rely heavily on the language of information, coding, and transmission that is commonplace in the field of information theory developed by Claude Shannon, but there is open debate about whether such language is anything more than facile metaphor. Philosophers of biology have argued that when biologists talk about information in genes and in evolution, they are not talking about the sort of information that Shannon's theory addresses. First, philosophers have suggested that Shannon's theory is only useful for developing a shallow notion of correlation, the so-called "causal sense" of information. Second, they typically argue that in genetics and evolutionary biology, information language is used in a "semantic sense," whereas semantics are deliberately omitted from Shannon's theory. Neither critique is well-founded. Here we propose an alternative to the causal and semantic senses of information: a transmission sense of information, in which an object X conveys information if the function of X is to reduce, by virtue of its sequence properties, uncertainty on the part of an agent who observes X. The transmission sense not only captures much of what biologists intend when they talk about information in genes, but also brings Shannon's theory back to the fore. By taking the viewpoint of a communications engineer and focusing on the decision problem of how information is to be packaged for transport, this approach resolves several problems that have plagued the information concept in biology, and highlights a number of important features of the way that information is encoded, stored, and transmitted as genetic sequence.[PUBLICATION ABSTRACT]; | |||||
BibTeX:
@article{bergstrom_transmission_2011,
author = {Bergstrom, Carl T. and Rosvall, Martin},
title = {The transmission sense of information},
journal = {Biology & Philosophy},
year = {2011},
volume = {26},
number = {2},
pages = {159--176},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlR3LTsMwzEKTkHbh_Sgv9bILoqhp1jQ9TjzEEfHYNWqSFiHGNo3tsH09drt0DzjAuW6b2I7fdgB4dB0GazIhC41I0kgYZpi0uc1MEXFOXZJo4WmzFtmGqI5k9D-uXYKylNtLrW8xTwMK7adMhsEMpTCqKirqe3ru1rKYtH013TsNuBSJy2v-9oUVzbQun5cSpWtDRUtFdL8NrkHGFaDUWelF3_zPAu1_bHAHtuY2qt-pmGoXNvL-HmxWt1ZO96D56K4_mO5DC_nMH5PCQ4ahyJv_hY5x7g8Kfz6TlSh_AK_3dy83D8H86oXAcBR_gUTH1RiBtofmGj3omBk6_UJIxrVMbWQE0xwPP7OJLqTJTWyNJW8MPSibhfwQGv1BPz8Gv9BxKtNE5zph7cKkWrSLKDNJlqHxqUPtwaVDuxpWEzbUYpYyIUEhEhQhQc08uCDCqKpJtD6diuPi0BiKpQdHJQBtETdvVp44Yirb6ynkP4nmWZQwD64cCZZWQD-m1JGaY7tawdAWHrR-gJMZ5d4RKiphCa7kkxqKRnnfvnc7ajB6U5PPiWrTNP-TP37vFJpVQJsK4M6gMR5N8vNqeuQ3PgD9Zw}
}
|
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| Barbieri, M. | Three Types of Semiosis | 2009 | Biosemiotics Vol. 2(1), pp. 19-30 |
article | |
| Abstract: The existence of different types of semiosis has been recognized, so far, in two ways. It has been pointed out that different semiotic features exist in different taxa and this has led to the distinction between zoosemiosis, phytosemiosis, mycosemiosis, bacterial semiosis and the like. Another type of diversity is due to the existence of different types of signs and has led to the distinction between iconic, indexical and symbolic semiosis. In all these cases, however, semiosis has been defined by the Peirce model, i.e., by the idea that the basic structure is a triad of 'sign, object and interpretant', and that interpretation is an essential component of semiosis. This model is undoubtedly applicable to animals, since it was precisely the discovery that animals are capable of interpretation that allowed Thomas Sebeok to conclude that they are also capable of semiosis. Unfortunately, however, it is not clear how far the Peirce model can be extended beyond the animal kingdom, and we already know that we cannot apply it to the cell. The rules of the genetic code have been virtually the same in all living systems and in all environments ever since the origin of life, which clearly shows that they do not depend on interpretation. Luckily, it has been pointed out that semiosis is not necessarily based on interpretation and can be defined exclusively in terms of coding. According to the 'code model', a semiotic system is made of signs, meanings and coding rules, all produced by the same codemaker, and in this form it is immediately applicable to the cell. The code model, furthermore, allows us to recognize the existence of many organic codes in living systems, and to divide them into two main types that here are referred to as manufacturing semiosis and signalling semiosis. The genetic code and the splicing codes, for example, take part in processes that actually manufacture biological objects, whereas signal transduction codes and compartment codes organize existing objects into functioning supramolecular structures. The organic codes of single cells appeared in the first three billion years of the history of life and were involved either in manufacturing semiosis or in signalling semiosis. With the origin of animals, however, a third type of semiosis came into being, a type that can be referred to as interpretive semiosis because it became closely involved with interpretation. We realize in this way that the contribution of semiosis to life was far greater than that predicted by the Peirce model, where semiosis is always a means of interpreting the world. Life is essentially about three things: (1) it is about manufacturing objects, (2) it is about organizing objects into functioning systems, and (3) it is about interpreting the world. The idea that these are all semiotic processes, tells us that life depends on semiosis much more deeply and extensively than we thought. We realize in this way that there are three distinct types of semiosis in Nature, and that they gave very different contributions to the origin and the evolution of life.;The existence of different types of semiosis has been recognized, so far, in two ways. It has been pointed out that different semiotic features exist in different taxa and this has led to the distinction between zoosemiosis, phytosemiosis, mycosemiosis, bacterial semiosis and the like. Another type of diversity is due to the existence of different types of signs and has led to the distinction between iconic, indexical and symbolic semiosis. In all these cases, however, semiosis has been defined by the Peirce model, i.e., by the idea that the basic structure is a triad of ‘sign, object and interpretant’, and that interpretation is an essential component of semiosis. This model is undoubtedly applicable to animals, since it was precisely the discovery that animals are capable of interpretation that allowed Thomas Sebeok to conclude that they are also capable of semiosis. Unfortunately, however, it is not clear how far the Peirce model can be extended beyond the animal kingdom, and we already know that we cannot apply it to the cell. The rules of the genetic code have been virtually the same in all living systems and in all environments ever since the origin of life, which clearly shows that they do not depend on interpretation. Luckily, it has been pointed out that semiosis is not necessarily based on interpretation and can be defined exclusively in terms of coding. According to the ‘code model’, a semiotic system is made of signs, meanings and coding rules, all produced by the same codemaker, and in this form it is immediately applicable to the cell. The code model, furthermore, allows us to recognize the existence of many organic codes in living systems, and to divide them into two main types that here are referred to as manufacturing semiosis and signalling semiosis. The genetic code and the splicing codes, for example, take part in processes that actually manufacture biological objects, whereas signal transduction codes and compartment codes organize existing objects into functioning supramolecular structures. The organic codes of single cells appeared in the first three billion years of the history of life and were involved either in manufacturing semiosis or in signalling semiosis. With the origin of animals, however, a third type of semiosis came into being, a type that can be referred to as interpretive semiosis because it became closely involved with interpretation. We realize in this way that the contribution of semiosis to life was far greater than that predicted by the Peirce model, where semiosis is always a means of interpreting the world. Life is essentially about three things: (1) it is about manufacturing objects, (2) it is about organizing objects into functioning systems, and (3) it is about interpreting the world. The idea that these are all semiotic processes, tells us that life depends on semiosis much more deeply and extensively than we thought. We realize in this way that there are three distinct types of semiosis in Nature, and that they gave very different contributions to the origin and the evolution of life.; | |||||
BibTeX:
@article{barbieri_three_2009,
author = {Barbieri, Marcello},
title = {Three Types of Semiosis},
journal = {Biosemiotics},
year = {2009},
volume = {2},
number = {1},
pages = {19--30}
}
|
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| Wheeler, M. | Traits, genes, and coding | 2007 | , pp. 369-399 | incollection | URL |
| Abstract: Genes are special biological component that contributes to an organism. However, the view that genes, or complexes of genes, code for phenotypic traits is a part of current biological orthodoxy. Coding talk about genes claims that genes are special developmental factors, and they count as being privileged causal elements in the developmental process. If the primary goal of introducing the concept of genetic coding is to single out genes as privileged causal elements in the developmental process, then it might well seem that any successful account of coding talk must have the consequence that, of the many causal factors that combine causally during development, the genes alone code for phenotypic traits. In recent years some of the most persistent critics of the idea that genes are informational entities that code for traits have come from the ranks of the developmental systems theorists. Those modifications in the components called genes-dramatically affect the structure. So it seems that if the representational theory of genes is tied to this condition, then the theory is straightforwardly undermined by the presence of developmental explanatory spread. Genes contain sequence of base pairs that are functionally redundant with respect to protein synthesis. © 2007 Elsevier B.V. All rights reserved. | |||||
BibTeX:
@incollection{wheeler_traits_2007,
author = {Wheeler, Michael},
title = {Traits, genes, and coding},
year = {2007},
pages = {369--399},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwzV1LS8QwEA6CKKIHn931Ab3oya5tp23SgxdfCLs3V_BWkjQrHlxXtoL-e2eatLtWvHtMC2E6CTPfpPm-YQziQRh0YgKXOlOxEjrnimdJbtI8SjD5JlmkU13qnyfbbZfSxbN_vvAdREzD0zhsj19tbDWO27d8IV62iemlqhfu2TiJfktraxNYU__zpfrfal8lpDGWJlY7xcUhsP1PXEoD24PoV7S0hftVLbLbzBIQKSAl5BeIRY5o_ot3Ukd7oS8mWbQM0dsZKZa_li-6ujTT4PEBkyMJ_lC1PBy1h19E70VkWisENNY3akhuLNy1K7qM17XwwtlH8q76bfYxX4IE4222STQRn_gbaOIOWzHTXbZmW3t-7bG-9fW5X3v63Ec_-9bP-2x8dzu-vg9cG4rACMACW4EBCVGJhekEVAkQk6ge4jBEjonimhRz8hCAp7nKcqlBSm5KpUwqJ2kI8QHbksRWmFY1q7H02OoEd5jxKN17aLXH1p_y0Y24H17b4U4zHMxr6t3gvfIQXdQbNMgGvMf8JJ1ERgkTCYWI1kS54pFC95TAJcQh9FnPuqaYWdWSol2iPjvtvirmcREWAoM5ok0BHIrqszr8e4ojtrHYisfue06skuU3qNclhA}
}
|
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| Mitrokhin, Y. | Two faces of entropy and information in biological systems | 2014 | Journal of theoretical biology Vol. 359, pp. 192-198 |
article | URL |
| Abstract: The article attempts to overcome the well-known paradox of contradictions between the emerging biological organization and entropy production in biological systems. It is assumed that quality, speculative correlation between entropy and antientropy processes taking place both in the past and today in the metabolic and genetic cellular systems may be perfectly authorized for adequate description of the evolution of biological organization. So far as thermodynamic entropy itself cannot compensate for the high degree of organization which exists in the cell, we discuss the mode of conjunction of positive entropy events (mutations) in the genetic systems of the past generations and the formation of organized structures of current cells. We argue that only the information which is generated in the conditions of the information entropy production (mutations and other genome reorganization) in genetic systems of the past generations provides the physical conjunction of entropy and antientropy processes separated from each other in time generations. It is readily apparent from the requirements of the Second law of thermodynamics.; The article attempts to overcome the well-known paradox of contradictions between the emerging biological organization and entropy production in biological systems. It is assumed that quality, speculative correlation between entropy and antientropy processes taking place both in the past and today in the metabolic and genetic cellular systems may be perfectly authorized for adequate description of the evolution of biological organization. So far as thermodynamic entropy itself cannot compensate for the high degree of organization which exists in the cell, we discuss the mode of conjunction of positive entropy events (mutations) in the genetic systems of the past generations and the formation of organized structures of current cells. We argue that only the information which is generated in the conditions of the information entropy production (mutations and other genome reorganization) in genetic systems of the past generations provides the physical conjunction of entropy and antientropy processes separated from each other in time generations. It is readily apparent from the requirements of the Second law of thermodynamics. © 2014 Elsevier Ltd.; The article attempts to overcome the well-known paradox of contradictions between the emerging biological organization and entropy production in biological systems. It is assumed that quality, speculative correlation between entropy and antientropy processes taking place both in the past and today in the metabolic and genetic cellular systems may be perfectly authorized for adequate description of the evolution of biological organization. So far as thermodynamic entropy itself cannot compensate for the high degree of organization which exists in the cell, we discuss the mode of conjunction of positive entropy events (mutations) in the genetic systems of the past generations and the formation of organized structures of current cells. We argue that only the information which is generated in the conditions of the information entropy production (mutations and other genome reorganization) in genetic systems of the past generations provides the physical conjunction of entropy and antientropy processes separated from each other in time generations. It is readily apparent from the requirements of the Second law of thermodynamics.; The article attempts to overcome the well-known paradox of contradictions between the emerging biological organization and entropy production in biological systems. It is assumed that quality, speculative correlation between entropy and antientropy processes taking place both in the past and today in the metabolic and genetic cellular systems may be perfectly authorized for adequate description of the evolution of biological organization. So far as thermodynamic entropy itself cannot compensate for the high degree of organization which exists in the cell, we discuss the mode of conjunction of positive entropy events (mutations) in the genetic systems of the past generations and the formation of organized structures of current cells. We argue that only the information which is generated in the conditions of the information entropy production (mutations and other genome reorganization) in genetic systems of the past generations provides the physical conjunction of entropy and antientropy processes separated from each other in time generations. It is readily apparent from the requirements of the Second law of thermodynamics. (C) 2014 Elsevier Ltd. All rights reserved. | |||||
BibTeX:
@article{mitrokhin_two_2014,
author = {Mitrokhin, Y.},
title = {Two faces of entropy and information in biological systems},
journal = {Journal of theoretical biology},
year = {2014},
volume = {359},
pages = {192--198},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV3JTsMwEB0hBBISYoeGRfKBGwQl2I0dblCo-IByjhIvhx7aqk2F-vfMxElKoUjllsiOJec5nhnnzRsA_vgQhT_2BKvR8JP2eN6VtD8qa0RUOJ4Y5yTXdvVkG-7_-KFfEbOGGNcTJ0tUwpsxJfoKwYnO1X99WQruiqo8YMVWJy-lTphZP8SKUaq35tYg7VB-yHy21jJVVqh_CA0Jv2GftL-kl0nzv9nZG83uCA5q15Q9-7V0DFt2dAK7vljl4hSeBp9j5ojBxcaO0aHweLJg-ciwWnyVIMZr5nWdCHzmdaJnZ_DRfxv03sO68kKoMWJ6DF3snC4w0su1UKaLUWQkrTNo8LoOHTjrtJGpo8rrQqEDKSV6LQ4dHVloh7Cm_Bz2c2Loj8oqk890gKU8tTJVRuXcCp1GKX6eujCqKDBkTJQM4K7BIJt4pY2soaANM3otGb2WjHh4sQrggmDKaIblNNcZV-g8YiyWYItHrh2FymsnnEcBdDyUbQuXXJACID50-x3ctkOl34NRM8Z5tJICiDfp1qvl1UlWoLz817yuYI_uPF3wGrbL6dzeeInILw4-9V8}
}
|
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| Shea, N. | What's transmitted? Inherited information | 2011 | Biology and Philosophy Vol. 26(2), pp. 183-189 |
article | URL |
| Abstract: Commentary on Bergstrom and Rosvall, 'The transmission sense of information', Biology and Philosophy. In response to worries that uses of the concept of information in biology are metaphorical or insubstantial, Bergstrom and Rosvall have identified a sense in which DNA transmits information down the generations. Their 'transmission view of information' is founded on a claim about DNA's teleofunction. Bergstrom and Rosvall see their transmission view of information as a rival to semantic accounts. This commentary argues that it is complementary. The idea that DNA is transmitting information down the generations only makes sense if it is carrying a message, that is to say if it has semantic content[PUBLICATION ABSTRACT]; Commentary on Bergstrom and Rosvall, 'The transmission sense of information', Biology and Philosophy. In response to worries that uses of the concept of information in biology are metaphorical or insubstantial, Bergstrom and Rosvall have identified a sense in which DNA transmits information down the generations. Their 'transmission view of information' is founded on a claim about DNA's teleofunction. Bergstrom and Rosvall see their transmission view of information as a rival to semantic accounts. This commentary argues that it is complementary. The idea that DNA is transmitting information down the generations only makes sense if it is carrying a message, that is to say if it has semantic content.; Commentary on Bergstrom and Rosvall, 'The transmission sense of information', Biology and Philosophy. In response to worries that uses of the concept of information in biology are metaphorical or insubstantial, Bergstrom and Rosvall have identified a sense in which DNA transmits information down the generations. Their 'transmission view of information' is founded on a claim about DNA's teleofunction. Bergstrom and Rosvall see their transmission view of information as a rival to semantic accounts. This commentary argues that it is complementary. The idea that DNA is transmitting information down the generations only makes sense if it is carrying a message, that is to say if it has semantic content Keywords Genetic information * Genetic representation * Inheritance systems * Information transmission * Natural selection * Evolution * Entropy; Commentary on Bergstrom and Rosvall, 'The transmission sense of information', Biology and Philosophy. In response to worries that uses of the concept of information in biology are metaphorical or insubstantial, Bergstrom and Rosvall have identified a sense in which DNA transmits information down the generations. Their 'transmission view of information' is founded on a claim about DNA's teleofunction. Bergstrom and Rosvall see their transmission view of information as a rival to semantic accounts. This commentary argues that it is complementary. The idea that DNA is transmitting information down the generations only makes sense if it is carrying a message, that is to say if it has semantic content | |||||
BibTeX:
@article{shea_whats_2011,
author = {Shea, Nicholas},
title = {What's transmitted? Inherited information},
journal = {Biology and Philosophy},
year = {2011},
volume = {26},
number = {2},
pages = {183--189},
url = {http://usyd.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw3V1bb9MwFLa4CDQJITYglJvywEU8pHLsxHUeEEKFqROTVtEN8WY1toMmbWVbPYn9e86x4zTteNgzj0msKPHnc7XPdwjhbEizDZ1gkPeJGVnVqDORFIvm0jCmmeGN8MRM_cx27IS3uvc_AI9k3D4L79AMnR47zGfyXdAEWOqHDmZLltpBEvd09_ymkl8M08ne_sHsYDrpPF1sfb3aujGrxCfv5wni6Yp-LlFUGZehG0ZUhqF8vQWd9TRbHvrNtEYyD31_rulfGuuRS47HsGgG_iNry3jWuK43bFB3MhA1dEVBy3C0pPwdEqCfmmPtPtpFdjS7DdG1xBj7–xHZ3DRpQsU7uF_4uZ1qJBc_5Lrlhc5YvXvs8vlP10P72YcPiIP2_gg_Rxw3Sa37GKH3AsdQ692yNY0tp64ekw-INTvl2kP6E9pB3Pag_kJOdr9ejieZG3ri-wXNiLJdA1hOhgAJGgsjK1yK7mmICmi0VLUFZ0XueGF1CBCBYTQBbNzPm8sFxb8ZVvyp-TBHEskFs6XUpqE3G1gWdsEfYwEfish939W-1_k5Ns4XG7Hy-HS1_sNz10CM-ylIhPD0TOSlppyI0vsTceKUtt6BM5-XVtZi7JhVAzIa5xcFUp4OxFSHAwH9rWhA5L4ATgBMDd67UkERJmTE8U4IMkhuMgH5G3AR50F_hXF1JIpqpDKENxniGEK5f44eMPGOIglaDES8Flv-sB2zzfW2oDkNxk2brnzkTPCPb_Zq1-QrZVIviR33MWlfRWIP_8C1iqLtA}
}
|
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| Shea, N. | What's transmitted? Inherited information.(DISCUSSION NOTE) [BibTeX] |
2011 | Biology & Philosophy Vol. 26(2), pp. 183 |
article | |
BibTeX:
@article{shea_whats_2011-1,
author = {Shea, Nicholas},
title = {What's transmitted? Inherited information.(DISCUSSION NOTE)},
journal = {Biology & Philosophy},
year = {2011},
volume = {26},
number = {2},
pages = {183}
}
|
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| Griffiths, P.E. and Wilkins, J.S. | When do evolutionary explanations of belief debunk belief? (preprint) [BibTeX] |
2010 | PhilSci Archive | article | URL |
BibTeX:
@article{griffiths_when_2010,
author = {Griffiths, Paul E. and Wilkins, John S.},
title = {When do evolutionary explanations of belief debunk belief? (preprint)},
journal = {PhilSci Archive},
year = {2010},
url = {http://philsci-archive.pitt.edu/5314/}
}
|
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Dr Bruce Long. PhD Philosophy, BA Hons 1 (Philosophy), M Phil. (English), B App Sc. (Computing).
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