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Kanai</a></div></div><div class="suggested-user-card"><div class="suggested-user-card__avatar social-profile-avatar-container"><a href="https://independent.academia.edu/MarcoJose"><img class="profile-avatar u-positionAbsolute" alt="Marco Jose" border="0" onerror="if (this.src != '//a.academia-assets.com/images/s200_no_pic.png') this.src = '//a.academia-assets.com/images/s200_no_pic.png';" width="200" height="200" src="https://0.academia-photos.com/4035558/1538197/1868000/s200_marco.jose.jpg" /></a></div><div class="suggested-user-card__user-info"><a class="suggested-user-card__user-info__header ds2-5-body-sm-bold ds2-5-body-link" href="https://independent.academia.edu/MarcoJose">Marco Jose</a></div></div><div class="suggested-user-card"><div class="suggested-user-card__avatar social-profile-avatar-container"><a href="https://independent.academia.edu/DasShib"><img class="profile-avatar u-positionAbsolute" border="0" alt="" src="//a.academia-assets.com/images/s200_no_pic.png" 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class="suggested-user-card__avatar social-profile-avatar-container"><a href="https://illinois.academia.edu/GustavoCaetanoAnolles"><img class="profile-avatar u-positionAbsolute" alt="Gustavo Caetano-Anolles" border="0" onerror="if (this.src != '//a.academia-assets.com/images/s200_no_pic.png') this.src = '//a.academia-assets.com/images/s200_no_pic.png';" width="200" height="200" src="https://0.academia-photos.com/32778210/18299108/18267179/s200_gustavo.caetano-anolles.jpg" /></a></div><div class="suggested-user-card__user-info"><a class="suggested-user-card__user-info__header ds2-5-body-sm-bold ds2-5-body-link" href="https://illinois.academia.edu/GustavoCaetanoAnolles">Gustavo Caetano-Anolles</a><p class="suggested-user-card__user-info__subheader ds2-5-body-xs">University of Illinois at Urbana-Champaign</p></div></div><div class="suggested-user-card"><div class="suggested-user-card__avatar social-profile-avatar-container"><a href="https://ucsc.academia.edu/DavidBernick"><img 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Environmental Microbiology"]}" data-trace="false" data-dom-id="Pill-react-component-157db5a6-c2c1-499b-bd6e-2c139ee73805"></div> <div id="Pill-react-component-157db5a6-c2c1-499b-bd6e-2c139ee73805"></div> </a><a data-click-track="profile-user-info-expand-research-interests" data-has-card-for-ri-list="78314817" href="https://www.academia.edu/Documents/in/Metagenomics"><div class="js-react-on-rails-component" style="display:none" data-component-name="Pill" data-props="{"color":"gray","children":["Metagenomics"]}" data-trace="false" data-dom-id="Pill-react-component-a1224a14-c9bc-4ab4-b3fd-8cd6ff192d51"></div> <div id="Pill-react-component-a1224a14-c9bc-4ab4-b3fd-8cd6ff192d51"></div> </a><a data-click-track="profile-user-info-expand-research-interests" data-has-card-for-ri-list="78314817" href="https://www.academia.edu/Documents/in/Molecular_dating"><div class="js-react-on-rails-component" style="display:none" data-component-name="Pill" data-props="{"color":"gray","children":["Molecular 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style="width: 100%;"><div class="u-taCenter"></div><div class="profile--tab_content_container js-tab-pane tab-pane active" id="all"><div class="profile--tab_heading_container js-section-heading" data-section="Papers" id="Papers"><h3 class="profile--tab_heading_container">Papers by Massimo Di Giulio</h3></div><div class="js-work-strip profile--work_container" data-work-id="125495843"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/125495843/is_Nanoarchaeum_equitans_a_paleokary_ote"><img alt="Research paper thumbnail of is Nanoarchaeum equitans a paleokary ote" class="work-thumbnail" src="https://attachments.academia-assets.com/119528161/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/125495843/is_Nanoarchaeum_equitans_a_paleokary_ote">is Nanoarchaeum equitans a paleokary ote</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Hypothesising the finding of an organism that still possesses a trait in an evolutionary state of...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Hypothesising the finding of an organism that still possesses a trait in an evolutionary state of tran sition, i.e. a paleokaryote (an organism that, for example, uses hairpins instead of complete tRNAs in the synthesis of its proteins), the aim of this paper is to clarify the singular, ancestral and, in some cases, unique characters possessed by Nanoarchaeum equitans. The absence of operons in the genome of N. equitans is considered as an ancestral transitional trait, which analysis equates to hairpins used by the hypothetical paleokaryote and thus leads to the following conclusions: (i) N. equitans might be the representative of a new phylum of Archaea; (ii) it is a living fossil; and (iii) it represents the root of the Archaea domain or of the tree of life (i.e. rooted in the Nanoarchaeota phylum). All these conclusions seem to be likely in light of the analysis here con ducted. Whereas, it is not equally clear whether N. equitans may be considered a true paleoka ryote and is the representative of a new domain of life, although these two possibilities might be supported by a further analysis of its biology.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="167f480f5db996efd9991a60c1736361" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":119528161,"asset_id":125495843,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/119528161/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="125495843"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="125495843"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 125495843; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="123290410"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/123290410/The_Early_Phases_of_Genetic_Code_Origin_Conjectures_on_the_Evolution_of_Coded_Catalysis"><img alt="Research paper thumbnail of The Early Phases of Genetic Code Origin: Conjectures on the Evolution of Coded Catalysis" class="work-thumbnail" src="https://attachments.academia-assets.com/117756800/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/123290410/The_Early_Phases_of_Genetic_Code_Origin_Conjectures_on_the_Evolution_of_Coded_Catalysis">The Early Phases of Genetic Code Origin: Conjectures on the Evolution of Coded Catalysis</a></div><div class="wp-workCard_item"><span>Origins of life and evolution of the biosphere</span><span>, 2004</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">A review of the most significant contributions on the early phases of genetic code origin is pres...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">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 s...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="e50bdbeb07356768c38c6c56251646c4" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":117756800,"asset_id":123290410,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/117756800/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290410"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290410"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290410; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="123290408"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/123290408/The_origin_of_the_tRNA_molecule_International_and_Interdisciplinary_Symposium_on_What_is_Evolution_Bicentennial_of_Charles_Darwins_Birth_"><img alt="Research paper thumbnail of The origin of the tRNA molecule(International & Interdisciplinary Symposium on What is Evolution? Bicentennial of Charles Darwin's Birth)" class="work-thumbnail" src="https://attachments.academia-assets.com/117756798/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/123290408/The_origin_of_the_tRNA_molecule_International_and_Interdisciplinary_Symposium_on_What_is_Evolution_Bicentennial_of_Charles_Darwins_Birth_">The origin of the tRNA molecule(International & Interdisciplinary Symposium on What is Evolution? Bicentennial of Charles Darwin's Birth)</a></div><div class="wp-workCard_item"><span>物性研究</span><span>, Apr 5, 2010</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="88fef8f9a2b3c9a7da6e8afdba2d7714" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":117756798,"asset_id":123290408,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/117756798/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290408"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290408"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290408; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=123290408]").text(description); $(".js-view-count[data-work-id=123290408]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 123290408; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='123290408']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "88fef8f9a2b3c9a7da6e8afdba2d7714" } } $('.js-work-strip[data-work-id=123290408]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":123290408,"title":"The origin of the tRNA molecule(International \u0026 Interdisciplinary Symposium on What is Evolution? 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This theory hypothesises a central role in enzyme catalysis played by peptidyl-RNAs, i.e. complexes of peptides and RNAs, in a very early evolutionary stage of genetic code origin. The evolution of peptidyl-RNA would then lead to the origin of peptidyl-tRNA, a key intermediary in the origin of protein synthesis. The appearance of the first mRNA might be justified by the need of the evolving system for unique and directional interactions between peptidyl-RNAs, which had now become peptidyl-tRNA-like molecules. The appearance of the first mRNA, would therefore be the result of the optimisation and channelling of interactions between peptidyl-tRNA-like molecules.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="6725ee35846d78f25eecb47249d55f1f" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":117756796,"asset_id":123290407,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/117756796/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290407"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290407"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290407; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="123290404"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/123290404/Special_issue_on_the_early_evolution_of_life"><img alt="Research paper thumbnail of Special issue on the early evolution of life" class="work-thumbnail" src="https://attachments.academia-assets.com/117756795/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/123290404/Special_issue_on_the_early_evolution_of_life">Special issue on the early evolution of life</a></div><div class="wp-workCard_item"><span>Journal of molecular evolution</span><span>, 2014</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">About a year ago, in late 2013, one of us (MDG) had the idea to put together a Special Issue of t...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">About a year ago, in late 2013, one of us (MDG) had the idea to put together a Special Issue of the Journal of Molecular Evolution dedicated to the Early Evolution of Life. At the time, the journal was receiving an increased number of submissions on this topic and in fact in recent months has been increasing its focus on very early molecular evolutionary events. Thus we decided to move forward with this idea, and the current issue (November/ December 2014) is the result of this current effort. Research into life's earliest periods is very dynamic, interdisciplinary, and at times highly speculative, given the antiquity of the events under study. Our best guess places the origins of life itself from chemical beginnings at roughly 4 billion years ago, with no physical evidence of life surviving that long. The earliest cells may have evolved on the Earth in the 3.5-4.0 Gya time frame, and evidence of these, although possible, is scarce at best. At some point prior to roughly 3.0 Gya, the last common universal ancestor (LUCA), which was a single ''species'' or, more probably, a highly reticulated network of genomic entities, came into being from whom all terrestrial life today is descended. Efforts to understand the events of the first billion years or so of life can be focused on a number of perspectives, including theoretical simulations, analyses of molecular ''fossils'' and/or phylogenetic clues, and empirical experiments in the laboratory. The articles in this Special Issue</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="b080c82db671c2b7adc4eb0d98eab1ee" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":117756795,"asset_id":123290404,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/117756795/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290404"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290404"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290404; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="123290403"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" rel="nofollow" href="https://www.academia.edu/123290403/The_genetic_code_did_not_originate_from_an_mRNA_codifying_polyglycine_because_the_proto_mRNAs_already_codified_for_an_amino_acid_number_greater_than_one"><img alt="Research paper thumbnail of The genetic code did not originate from an mRNA codifying polyglycine because the proto-mRNAs already codified for an amino acid number greater than one" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" rel="nofollow" href="https://www.academia.edu/123290403/The_genetic_code_did_not_originate_from_an_mRNA_codifying_polyglycine_because_the_proto_mRNAs_already_codified_for_an_amino_acid_number_greater_than_one">The genetic code did not originate from an mRNA codifying polyglycine because the proto-mRNAs already codified for an amino acid number greater than one</a></div><div class="wp-workCard_item"><span>Journal of theoretical biology</span><span>, Jan 21, 2014</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">I reply to Bernhart and Patrick (2014) that claim that the first amino acid to be codified in the...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">I reply to Bernhart and Patrick (2014) that claim that the first amino acid to be codified in the genetic code was glycine, and that from mRNAs codifying for polyglycine originated all other codons of the genetic code. Indeed, given that the origin of protein synthesis should have preceded the one of the genetic code, then proto-mRNAs codifying for polimeric catalysts of the world in which originated the protein synthesis, should have been the more direct ancestors of mRNAs that originated in the world in which evolved the true genetic code. Therefore, it is clear that there would have been at least a partial evolutionary continuity between these proto-mRNAs and mRNAs. This evolutionary continuity has as logical consequence that cannot have existed of mRNAs codifying for only an amino acid because these mRNAs would descend from proto-mRNAs that already codified for more than one amino acid. Therefore, these mRNAs would not have reshaped their codifying capability to a single amino a...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290403"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290403"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290403; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=123290403]").text(description); $(".js-view-count[data-work-id=123290403]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 123290403; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='123290403']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=123290403]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":123290403,"title":"The genetic code did not originate from an mRNA codifying polyglycine because the proto-mRNAs already codified for an amino acid number greater than one","internal_url":"https://www.academia.edu/123290403/The_genetic_code_did_not_originate_from_an_mRNA_codifying_polyglycine_because_the_proto_mRNAs_already_codified_for_an_amino_acid_number_greater_than_one","owner_id":78314817,"coauthors_can_edit":true,"owner":{"id":78314817,"first_name":"Massimo","middle_initials":null,"last_name":"Di Giulio","page_name":"MassimoDiGiulio","domain_name":"independent","created_at":"2018-03-11T07:50:42.526-07:00","display_name":"Massimo Di Giulio","url":"https://independent.academia.edu/MassimoDiGiulio"},"attachments":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="123290401"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" rel="nofollow" href="https://www.academia.edu/123290401/The_Origin_of_the_Genetic_Code_cannot_be_Studied_using_Measurements_based_on_the_PAM_Matrix_because_this_Matrix_Reflects_the_Code_Itself_Making_any_such_Analyses_Tautologous"><img alt="Research paper thumbnail of The Origin of the Genetic Code cannot be Studied using Measurements based on the PAM Matrix because this Matrix Reflects the Code Itself, Making any such Analyses Tautologous" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" rel="nofollow" href="https://www.academia.edu/123290401/The_Origin_of_the_Genetic_Code_cannot_be_Studied_using_Measurements_based_on_the_PAM_Matrix_because_this_Matrix_Reflects_the_Code_Itself_Making_any_such_Analyses_Tautologous">The Origin of the Genetic Code cannot be Studied using Measurements based on the PAM Matrix because this Matrix Reflects the Code Itself, Making any such Analyses Tautologous</a></div><div class="wp-workCard_item"><span>Journal of Theoretical Biology</span><span>, 2001</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Freeland et al. (Mol. Biol. Evol. 2000 a, 17, 511--518) have recently used a transformation of th...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Freeland et al. (Mol. Biol. Evol. 2000 a, 17, 511--518) have recently used a transformation of the PAM 74-100 matrix to study the level of optimization reached during genetic code origin. Since the PAM matrix counts the amino acid substitutions that occurred in families of homologous proteins during molecular evolution and as this process is mediated by the genetic code structure itself, it could be that the influence of the code on this matrix is such as to make any conclusion insignificant. As will be shown in the present paper, the transformation of the PAM matrix is affected in a non-marginal way by the organization of the genetic code and, thus, renders the analysis of Freeland et al. tautologous. Although, under the hypothesis of a highly optimized genetic code, some correlations may be expected between a measurement of similarity between amino acids and the genetic code structure, no certain conclusions can be drawn for the measurement used by Freeland et al.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290401"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290401"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290401; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="123290399"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/123290399/The_Non_monophyletic_Origin_of_the_tRNA_Molecule"><img alt="Research paper thumbnail of The Non-monophyletic Origin of the tRNA Molecule" class="work-thumbnail" src="https://attachments.academia-assets.com/117756794/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/123290399/The_Non_monophyletic_Origin_of_the_tRNA_Molecule">The Non-monophyletic Origin of the tRNA Molecule</a></div><div class="wp-workCard_item"><span>Journal of Theoretical Biology</span><span>, 1999</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="bd907fface001646458129f7cab486a3" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":117756794,"asset_id":123290399,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/117756794/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290399"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290399"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290399; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="123290395"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/123290395/The_non_monophyletic_origin_of_the_tRNA_molecule_and_the_origin_of_genes_only_after_the_evolutionary_stage_of_the_last_universal_common_ancestor_LUCA_"><img alt="Research paper thumbnail of The non-monophyletic origin of the tRNA molecule and the origin of genes only after the evolutionary stage of the last universal common ancestor (LUCA)" class="work-thumbnail" src="https://attachments.academia-assets.com/117756793/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/123290395/The_non_monophyletic_origin_of_the_tRNA_molecule_and_the_origin_of_genes_only_after_the_evolutionary_stage_of_the_last_universal_common_ancestor_LUCA_">The non-monophyletic origin of the tRNA molecule and the origin of genes only after the evolutionary stage of the last universal common ancestor (LUCA)</a></div><div class="wp-workCard_item"><span>Journal of Theoretical Biology</span><span>, 2006</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">A model has been proposed suggesting that the tRNA molecule must have originated by direct duplic...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">A model has been proposed suggesting that the tRNA molecule must have originated by direct duplication of an RNA hairpin structure On the origin of the transfer RNA molecule. J. Theor. Biol. 159,[199][200][201][202][203][204][205][206][207][208][209][210][211][212][213][214]. A non-monophyletic origin of this molecule has also been theorized . The non-monophyletic origin of tRNA molecule. J. Theor. Biol. 197,[403][404][405][406][407][408][409][410][411][412][413][414]. In other words, the tRNA genes evolved only after the evolutionary stage of the last universal common ancestor (LUCA) through the assembly of two minigenes codifying for different RNA hairpin structures, which is what the exon theory of genes suggests when it is applied to the model of tRNA origin. Recent observations strongly corroborate this theorization because it has been found that some tRNA genes are completely separate in two minigenes codifying for the 5 0 and 3 0 halves of this molecule [Randau, L., et al., 2005a. Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5 0 -and 3 0 -halves. Nature 433, 537-541]. In this paper it is shown that these tRNA genes codifying for the 5 0 and 3 0 halves of this molecule are the ancestral form from which the tRNA genes continuously codifying for the complete tRNA molecule are thought to have evolved. This, together with the very existence of completely separate tRNA genes codifying for their 5 0 and 3 0 halves, proves a non-monophyletic origin for tRNA genes, as a monophyletic origin would exclude the existence of these genes which have, on the contrary, been observed. Here the polyphyletic origin of genes codifying for proteins is also suggested and discussed. Moreover, a hypothesis is advanced to suggest that the LUCA might have had a fragmented genome made up of RNA and the possibility that 'Paleokaryotes' may exist is outlined. Finally, the characteristic of the indivisibility of homology that these polyphyletic origins seem to remove at the sequence level is discussed.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="f478eeee013c0e5f76ad5e1c213087d0" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":117756793,"asset_id":123290395,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/117756793/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290395"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290395"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290395; 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It seems that a molecule capable of assuming a hairpin structure was involved as a precursor in this duplication. The two halves of the present tRNAs could, therefore, be considered as paralogous.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290393"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290393"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290393; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=123290393]").text(description); 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="123290391"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/123290391/The_universal_ancestor_was_a_thermophile_or_a_hyperthermophile"><img alt="Research paper thumbnail of The universal ancestor was a thermophile or a hyperthermophile" class="work-thumbnail" src="https://attachments.academia-assets.com/117756789/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/123290391/The_universal_ancestor_was_a_thermophile_or_a_hyperthermophile">The universal ancestor was a thermophile or a hyperthermophile</a></div><div class="wp-workCard_item"><span>Gene</span><span>, 2001</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">By exploiting the correlation between the optimal growth temperature of organisms and a thermophi...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">By exploiting the correlation between the optimal growth temperature of organisms and a thermophily index based on the propensity of amino acids to enter thermophile/hyperthermophile proteins, an analysis is conducted in order to establish whether the last universal common ancestor (LUCA) was a mesophile or a (hyper)thermophile. This objective is reached by using maximum parsimony and maximum likelihood to reconstruct the ancestral sequences of the LUCA for two pairs of sets of paralogous protein sequences by means of the phylogenetic tree topology derived from the small subunit ribosomal RNA, even if this is rooted in all three possible ways. The thermophily index of all the reconstructed ancestral sequences of the LUCA belongs to the set of the thermophile/hyperthermophile sequences, thus supporting the hypotheses that see the LUCA as a thermophile or a hyperthermophile.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="fe7b7a6188acf780e47acb51d7ca811d" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":117756789,"asset_id":123290391,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/117756789/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290391"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290391"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290391; 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</script> <div class="js-work-strip profile--work_container" data-work-id="123290387"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/123290387/The_first_lines_of_divergence_in_the_Bacteria_domain_seem_to_be_the_hyperthermophilic_organisms_a_check_using_an_outgroup_of_sequences_from_mesophiles_in_phylogenetic_analysis"><img alt="Research paper thumbnail of The first lines of divergence in the Bacteria domain seem to be the hyperthermophilic organisms: a check using an outgroup of sequences from mesophiles in phylogenetic analysis" class="work-thumbnail" src="https://attachments.academia-assets.com/117756788/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/123290387/The_first_lines_of_divergence_in_the_Bacteria_domain_seem_to_be_the_hyperthermophilic_organisms_a_check_using_an_outgroup_of_sequences_from_mesophiles_in_phylogenetic_analysis">The first lines of divergence in the Bacteria domain seem to be the hyperthermophilic organisms: a check using an outgroup of sequences from mesophiles in phylogenetic analysis</a></div><div class="wp-workCard_item"><span>Annals of Microbiology</span><span>, 2007</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="62d7701918bab5c4ef11312d6284fc51" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":117756788,"asset_id":123290387,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/117756788/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290387"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290387"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290387; 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The results, although not conclusive, indicate that this optimization level is higher than the data reported in the literature. The results seem compatible with the reaching of an evolutionary minimum, with respect to the optimization of the polarity distances, by the genetic code during its formation.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="347b23868498c9289c9efaa0aaf62f1a" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":117756741,"asset_id":123290340,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/117756741/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290340"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290340"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290340; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=123290340]").text(description); $(".js-view-count[data-work-id=123290340]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 123290340; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='123290340']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="119604158"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/119604158/The_Robust_Statistical_Bases_of_the_Coevolution_Theory_of_Genetic_Code_Origin"><img alt="Research paper thumbnail of The Robust Statistical Bases of the Coevolution Theory of Genetic Code Origin" class="work-thumbnail" src="https://attachments.academia-assets.com/114985394/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/119604158/The_Robust_Statistical_Bases_of_the_Coevolution_Theory_of_Genetic_Code_Origin">The Robust Statistical Bases of the Coevolution Theory of Genetic Code Origin</a></div><div class="wp-workCard_item"><span>Journal of Molecular Evolution</span><span>, 2000</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">A paper (Amirnovin R, J Mol Evol 44:473-476, 1997) seems to undermine the validity of the coevolu...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">A paper (Amirnovin R, J Mol Evol 44:473-476, 1997) seems to undermine the validity of the coevolution theory of genetic code origin by shedding doubt on the connection between the biosynthetic relationships between amino acids and the organization of the genetic code, at a time when the literature on the topic takes this for granted. However, as a few papers cite this paper as evidence against the coevolution theory, and to cast aside all doubt on the subject, we have decided to reanalyze the statistical bases on which this theory is founded. We come to the following conclusions: (1) the methods used in the above referred paper contain certain mistakes, and (2) the statistical foundations on which the coevolution theory is based are extremely robust. We have done this by critically appraising Amirnovin's paper and suggesting an alternative method based on the generation of random codes which, along with the method reported in the literature, allows us to evaluate the significance, in the genetic code, of different sets of amino acid pairs in biosynthetic relationships. In particular, by using this method and after building up a certain set of amino acid pairs reflecting the expectations of the coevolution theory, we show that the presence of this set in the genetic code would be obtained, purely by chance, with a probability of 6 × 10 −5. This observation seems to provide particularly strong support to the coevolution theory.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="dc077dc8ab8bfed32be38be16283d310" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":114985394,"asset_id":119604158,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/114985394/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="119604158"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="119604158"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 119604158; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="119604157"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" rel="nofollow" href="https://www.academia.edu/119604157/On_the_Optimization_of_the_Physicochemical_Distances_between_Amino_Acids_in_the_Evolution_of_the_Genetic_Code"><img alt="Research paper thumbnail of On the Optimization of the Physicochemical Distances between Amino Acids in the Evolution of the Genetic Code" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" rel="nofollow" href="https://www.academia.edu/119604157/On_the_Optimization_of_the_Physicochemical_Distances_between_Amino_Acids_in_the_Evolution_of_the_Genetic_Code">On the Optimization of the Physicochemical Distances between Amino Acids in the Evolution of the Genetic Code</a></div><div class="wp-workCard_item"><span>Journal of Theoretical Biology</span><span>, 1994</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Using the simulated annealing technique we re-examine the role played by the minimization of the ...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Using the simulated annealing technique we re-examine the role played by the minimization of the physicochemical distances between amino acids during the origin of the organization of the genetic code. The results are discussed in the context of the various hypotheses proposed to explain how amino acids were allocated in the genetic code.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="119604157"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="119604157"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 119604157; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=119604157]").text(description); $(".js-view-count[data-work-id=119604157]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 119604157; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='119604157']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=119604157]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":119604157,"title":"On the Optimization of the Physicochemical Distances between Amino Acids in the Evolution of the Genetic Code","internal_url":"https://www.academia.edu/119604157/On_the_Optimization_of_the_Physicochemical_Distances_between_Amino_Acids_in_the_Evolution_of_the_Genetic_Code","owner_id":78314817,"coauthors_can_edit":true,"owner":{"id":78314817,"first_name":"Massimo","middle_initials":null,"last_name":"Di Giulio","page_name":"MassimoDiGiulio","domain_name":"independent","created_at":"2018-03-11T07:50:42.526-07:00","display_name":"Massimo Di Giulio","url":"https://independent.academia.edu/MassimoDiGiulio"},"attachments":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="119604156"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/119604156/The_Historical_Factor_The_Biosynthetic_Relationships_Between_Amino_Acids_and_Their_Physicochemical_Properties_in_the_Origin_of_the_Genetic_Code"><img alt="Research paper thumbnail of The Historical Factor: The Biosynthetic Relationships Between Amino Acids and Their Physicochemical Properties in the Origin of the Genetic Code" class="work-thumbnail" src="https://attachments.academia-assets.com/114985395/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/119604156/The_Historical_Factor_The_Biosynthetic_Relationships_Between_Amino_Acids_and_Their_Physicochemical_Properties_in_the_Origin_of_the_Genetic_Code">The Historical Factor: The Biosynthetic Relationships Between Amino Acids and Their Physicochemical Properties in the Origin of the Genetic Code</a></div><div class="wp-workCard_item"><span>Journal of Molecular Evolution</span><span>, 1998</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Two forces are in general, hypothesized to have influenced the origin of the organization of the ...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Two forces are in general, hypothesized to have influenced the origin of the organization of the genetic code: the physicochemical properties of amino acids and their biosynthetic relationships. In view of this, we have considered a model incorporating these two forces. In particular, we have studied the optimization level of the physicochemical properties of amino acids in the set of amino acid permutation codes that respects the biosynthetic relationships between amino acids. Where the properties of amino acids are represented by polarity and molecular volume we obtain indetermination percentages in the organization of the genetic code of approximately 40%. This indicates that the contingent factor played a significant role in structuring the genetic code. Furthermore, this result is in agreement with the genetic code coevolution hypothesis, which attributes a merely ancillary role to the properties of amino acids while it suggests that it was their biosynthetic relationships that organized the code. Furthermore, this result does not favor the stereochemical models proposed to explain the origin of the genetic code. On the other hand, where the properties of amino acids are represented by polarity alone, we obtain an indetermination percentage of at least 21.5%. This might suggest that the polarity distances played an important role and would therefore provide evidence in favor of the physicochemical hypothesis of genetic code origin. Although, overall, the analysis might have given stronger support to the latter hypothesis, this did not actually occur. The results are therefore discussed in the context of the different theories proposed to explain the origin of the genetic code.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="057b603702684648401abcfa48cdabd3" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":114985395,"asset_id":119604156,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/114985395/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="119604156"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="119604156"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 119604156; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="115960029"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/115960029/Some_aspects_of_the_organization_and_evolution_of_the_genetic_code"><img alt="Research paper thumbnail of Some aspects of the organization and evolution of the genetic code" class="work-thumbnail" src="https://attachments.academia-assets.com/112222789/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/115960029/Some_aspects_of_the_organization_and_evolution_of_the_genetic_code">Some aspects of the organization and evolution of the genetic code</a></div><div class="wp-workCard_item"><span>Journal of Molecular Evolution</span><span>, 1989</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">In this paper, I define a measure of the relative position of each amino acid in the genetic code...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">In this paper, I define a measure of the relative position of each amino acid in the genetic code by means of a 21-dimensional vector describing its potential for mutation, in a single step, to each of the other amino acids, or to a chain termination codon. This measure allows us to make a systematic investigation of the type and number of the physicochemical properties of the amino acids that were involved in evolution. The polar character and size of amino acids are identified in this analysis as properties that played a leading role in the evolutionary history of the genetic code. The application of cluster analysis and discriminant analysis reveals the characteristics of the structural organization of the genetic code. Finally, I suggest the existence of a relationship between the molecular weight of the amino acids and the number of synonymous codons.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="b4b1735ab0a7da4d91db430227c87473" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":112222789,"asset_id":115960029,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/112222789/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="115960029"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="115960029"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 115960029; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> </div><div class="profile--tab_content_container js-tab-pane tab-pane" data-section-id="8092757" id="papers"><div class="js-work-strip profile--work_container" data-work-id="125495843"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/125495843/is_Nanoarchaeum_equitans_a_paleokary_ote"><img alt="Research paper thumbnail of is Nanoarchaeum equitans a paleokary ote" class="work-thumbnail" src="https://attachments.academia-assets.com/119528161/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/125495843/is_Nanoarchaeum_equitans_a_paleokary_ote">is Nanoarchaeum equitans a paleokary ote</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Hypothesising the finding of an organism that still possesses a trait in an evolutionary state of...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Hypothesising the finding of an organism that still possesses a trait in an evolutionary state of tran sition, i.e. a paleokaryote (an organism that, for example, uses hairpins instead of complete tRNAs in the synthesis of its proteins), the aim of this paper is to clarify the singular, ancestral and, in some cases, unique characters possessed by Nanoarchaeum equitans. The absence of operons in the genome of N. equitans is considered as an ancestral transitional trait, which analysis equates to hairpins used by the hypothetical paleokaryote and thus leads to the following conclusions: (i) N. equitans might be the representative of a new phylum of Archaea; (ii) it is a living fossil; and (iii) it represents the root of the Archaea domain or of the tree of life (i.e. rooted in the Nanoarchaeota phylum). All these conclusions seem to be likely in light of the analysis here con ducted. Whereas, it is not equally clear whether N. equitans may be considered a true paleoka ryote and is the representative of a new domain of life, although these two possibilities might be supported by a further analysis of its biology.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="167f480f5db996efd9991a60c1736361" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":119528161,"asset_id":125495843,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/119528161/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="125495843"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="125495843"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 125495843; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="123290410"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/123290410/The_Early_Phases_of_Genetic_Code_Origin_Conjectures_on_the_Evolution_of_Coded_Catalysis"><img alt="Research paper thumbnail of The Early Phases of Genetic Code Origin: Conjectures on the Evolution of Coded Catalysis" class="work-thumbnail" src="https://attachments.academia-assets.com/117756800/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/123290410/The_Early_Phases_of_Genetic_Code_Origin_Conjectures_on_the_Evolution_of_Coded_Catalysis">The Early Phases of Genetic Code Origin: Conjectures on the Evolution of Coded Catalysis</a></div><div class="wp-workCard_item"><span>Origins of life and evolution of the biosphere</span><span>, 2004</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">A review of the most significant contributions on the early phases of genetic code origin is pres...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">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 s...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="e50bdbeb07356768c38c6c56251646c4" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":117756800,"asset_id":123290410,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/117756800/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290410"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290410"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290410; 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Bicentennial of Charles Darwin's Birth)" class="work-thumbnail" src="https://attachments.academia-assets.com/117756798/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/123290408/The_origin_of_the_tRNA_molecule_International_and_Interdisciplinary_Symposium_on_What_is_Evolution_Bicentennial_of_Charles_Darwins_Birth_">The origin of the tRNA molecule(International & Interdisciplinary Symposium on What is Evolution? 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This theory hypothesises a central role in enzyme catalysis played by peptidyl-RNAs, i.e. complexes of peptides and RNAs, in a very early evolutionary stage of genetic code origin. The evolution of peptidyl-RNA would then lead to the origin of peptidyl-tRNA, a key intermediary in the origin of protein synthesis. The appearance of the first mRNA might be justified by the need of the evolving system for unique and directional interactions between peptidyl-RNAs, which had now become peptidyl-tRNA-like molecules. The appearance of the first mRNA, would therefore be the result of the optimisation and channelling of interactions between peptidyl-tRNA-like molecules.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="6725ee35846d78f25eecb47249d55f1f" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":117756796,"asset_id":123290407,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/117756796/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290407"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290407"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290407; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="123290404"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/123290404/Special_issue_on_the_early_evolution_of_life"><img alt="Research paper thumbnail of Special issue on the early evolution of life" class="work-thumbnail" src="https://attachments.academia-assets.com/117756795/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/123290404/Special_issue_on_the_early_evolution_of_life">Special issue on the early evolution of life</a></div><div class="wp-workCard_item"><span>Journal of molecular evolution</span><span>, 2014</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">About a year ago, in late 2013, one of us (MDG) had the idea to put together a Special Issue of t...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">About a year ago, in late 2013, one of us (MDG) had the idea to put together a Special Issue of the Journal of Molecular Evolution dedicated to the Early Evolution of Life. At the time, the journal was receiving an increased number of submissions on this topic and in fact in recent months has been increasing its focus on very early molecular evolutionary events. Thus we decided to move forward with this idea, and the current issue (November/ December 2014) is the result of this current effort. Research into life's earliest periods is very dynamic, interdisciplinary, and at times highly speculative, given the antiquity of the events under study. Our best guess places the origins of life itself from chemical beginnings at roughly 4 billion years ago, with no physical evidence of life surviving that long. The earliest cells may have evolved on the Earth in the 3.5-4.0 Gya time frame, and evidence of these, although possible, is scarce at best. At some point prior to roughly 3.0 Gya, the last common universal ancestor (LUCA), which was a single ''species'' or, more probably, a highly reticulated network of genomic entities, came into being from whom all terrestrial life today is descended. Efforts to understand the events of the first billion years or so of life can be focused on a number of perspectives, including theoretical simulations, analyses of molecular ''fossils'' and/or phylogenetic clues, and empirical experiments in the laboratory. The articles in this Special Issue</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="b080c82db671c2b7adc4eb0d98eab1ee" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":117756795,"asset_id":123290404,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/117756795/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290404"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290404"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290404; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="123290403"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" rel="nofollow" href="https://www.academia.edu/123290403/The_genetic_code_did_not_originate_from_an_mRNA_codifying_polyglycine_because_the_proto_mRNAs_already_codified_for_an_amino_acid_number_greater_than_one"><img alt="Research paper thumbnail of The genetic code did not originate from an mRNA codifying polyglycine because the proto-mRNAs already codified for an amino acid number greater than one" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" rel="nofollow" href="https://www.academia.edu/123290403/The_genetic_code_did_not_originate_from_an_mRNA_codifying_polyglycine_because_the_proto_mRNAs_already_codified_for_an_amino_acid_number_greater_than_one">The genetic code did not originate from an mRNA codifying polyglycine because the proto-mRNAs already codified for an amino acid number greater than one</a></div><div class="wp-workCard_item"><span>Journal of theoretical biology</span><span>, Jan 21, 2014</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">I reply to Bernhart and Patrick (2014) that claim that the first amino acid to be codified in the...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">I reply to Bernhart and Patrick (2014) that claim that the first amino acid to be codified in the genetic code was glycine, and that from mRNAs codifying for polyglycine originated all other codons of the genetic code. Indeed, given that the origin of protein synthesis should have preceded the one of the genetic code, then proto-mRNAs codifying for polimeric catalysts of the world in which originated the protein synthesis, should have been the more direct ancestors of mRNAs that originated in the world in which evolved the true genetic code. Therefore, it is clear that there would have been at least a partial evolutionary continuity between these proto-mRNAs and mRNAs. This evolutionary continuity has as logical consequence that cannot have existed of mRNAs codifying for only an amino acid because these mRNAs would descend from proto-mRNAs that already codified for more than one amino acid. Therefore, these mRNAs would not have reshaped their codifying capability to a single amino a...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290403"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290403"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290403; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=123290403]").text(description); $(".js-view-count[data-work-id=123290403]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 123290403; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='123290403']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=123290403]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":123290403,"title":"The genetic code did not originate from an mRNA codifying polyglycine because the proto-mRNAs already codified for an amino acid number greater than one","internal_url":"https://www.academia.edu/123290403/The_genetic_code_did_not_originate_from_an_mRNA_codifying_polyglycine_because_the_proto_mRNAs_already_codified_for_an_amino_acid_number_greater_than_one","owner_id":78314817,"coauthors_can_edit":true,"owner":{"id":78314817,"first_name":"Massimo","middle_initials":null,"last_name":"Di Giulio","page_name":"MassimoDiGiulio","domain_name":"independent","created_at":"2018-03-11T07:50:42.526-07:00","display_name":"Massimo Di Giulio","url":"https://independent.academia.edu/MassimoDiGiulio"},"attachments":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="123290401"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" rel="nofollow" href="https://www.academia.edu/123290401/The_Origin_of_the_Genetic_Code_cannot_be_Studied_using_Measurements_based_on_the_PAM_Matrix_because_this_Matrix_Reflects_the_Code_Itself_Making_any_such_Analyses_Tautologous"><img alt="Research paper thumbnail of The Origin of the Genetic Code cannot be Studied using Measurements based on the PAM Matrix because this Matrix Reflects the Code Itself, Making any such Analyses Tautologous" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" rel="nofollow" href="https://www.academia.edu/123290401/The_Origin_of_the_Genetic_Code_cannot_be_Studied_using_Measurements_based_on_the_PAM_Matrix_because_this_Matrix_Reflects_the_Code_Itself_Making_any_such_Analyses_Tautologous">The Origin of the Genetic Code cannot be Studied using Measurements based on the PAM Matrix because this Matrix Reflects the Code Itself, Making any such Analyses Tautologous</a></div><div class="wp-workCard_item"><span>Journal of Theoretical Biology</span><span>, 2001</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Freeland et al. (Mol. Biol. Evol. 2000 a, 17, 511--518) have recently used a transformation of th...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Freeland et al. (Mol. Biol. Evol. 2000 a, 17, 511--518) have recently used a transformation of the PAM 74-100 matrix to study the level of optimization reached during genetic code origin. Since the PAM matrix counts the amino acid substitutions that occurred in families of homologous proteins during molecular evolution and as this process is mediated by the genetic code structure itself, it could be that the influence of the code on this matrix is such as to make any conclusion insignificant. As will be shown in the present paper, the transformation of the PAM matrix is affected in a non-marginal way by the organization of the genetic code and, thus, renders the analysis of Freeland et al. tautologous. Although, under the hypothesis of a highly optimized genetic code, some correlations may be expected between a measurement of similarity between amino acids and the genetic code structure, no certain conclusions can be drawn for the measurement used by Freeland et al.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290401"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290401"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290401; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="123290399"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/123290399/The_Non_monophyletic_Origin_of_the_tRNA_Molecule"><img alt="Research paper thumbnail of The Non-monophyletic Origin of the tRNA Molecule" class="work-thumbnail" src="https://attachments.academia-assets.com/117756794/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/123290399/The_Non_monophyletic_Origin_of_the_tRNA_Molecule">The Non-monophyletic Origin of the tRNA Molecule</a></div><div class="wp-workCard_item"><span>Journal of Theoretical Biology</span><span>, 1999</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="bd907fface001646458129f7cab486a3" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":117756794,"asset_id":123290399,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/117756794/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290399"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290399"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290399; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="123290395"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/123290395/The_non_monophyletic_origin_of_the_tRNA_molecule_and_the_origin_of_genes_only_after_the_evolutionary_stage_of_the_last_universal_common_ancestor_LUCA_"><img alt="Research paper thumbnail of The non-monophyletic origin of the tRNA molecule and the origin of genes only after the evolutionary stage of the last universal common ancestor (LUCA)" class="work-thumbnail" src="https://attachments.academia-assets.com/117756793/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/123290395/The_non_monophyletic_origin_of_the_tRNA_molecule_and_the_origin_of_genes_only_after_the_evolutionary_stage_of_the_last_universal_common_ancestor_LUCA_">The non-monophyletic origin of the tRNA molecule and the origin of genes only after the evolutionary stage of the last universal common ancestor (LUCA)</a></div><div class="wp-workCard_item"><span>Journal of Theoretical Biology</span><span>, 2006</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">A model has been proposed suggesting that the tRNA molecule must have originated by direct duplic...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">A model has been proposed suggesting that the tRNA molecule must have originated by direct duplication of an RNA hairpin structure On the origin of the transfer RNA molecule. J. Theor. Biol. 159,[199][200][201][202][203][204][205][206][207][208][209][210][211][212][213][214]. A non-monophyletic origin of this molecule has also been theorized . The non-monophyletic origin of tRNA molecule. J. Theor. Biol. 197,[403][404][405][406][407][408][409][410][411][412][413][414]. In other words, the tRNA genes evolved only after the evolutionary stage of the last universal common ancestor (LUCA) through the assembly of two minigenes codifying for different RNA hairpin structures, which is what the exon theory of genes suggests when it is applied to the model of tRNA origin. Recent observations strongly corroborate this theorization because it has been found that some tRNA genes are completely separate in two minigenes codifying for the 5 0 and 3 0 halves of this molecule [Randau, L., et al., 2005a. Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5 0 -and 3 0 -halves. Nature 433, 537-541]. In this paper it is shown that these tRNA genes codifying for the 5 0 and 3 0 halves of this molecule are the ancestral form from which the tRNA genes continuously codifying for the complete tRNA molecule are thought to have evolved. This, together with the very existence of completely separate tRNA genes codifying for their 5 0 and 3 0 halves, proves a non-monophyletic origin for tRNA genes, as a monophyletic origin would exclude the existence of these genes which have, on the contrary, been observed. Here the polyphyletic origin of genes codifying for proteins is also suggested and discussed. Moreover, a hypothesis is advanced to suggest that the LUCA might have had a fragmented genome made up of RNA and the possibility that 'Paleokaryotes' may exist is outlined. Finally, the characteristic of the indivisibility of homology that these polyphyletic origins seem to remove at the sequence level is discussed.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="f478eeee013c0e5f76ad5e1c213087d0" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":117756793,"asset_id":123290395,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/117756793/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290395"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290395"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290395; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="123290393"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" rel="nofollow" href="https://www.academia.edu/123290393/On_the_origin_of_the_transfer_RNA_molecule"><img alt="Research paper thumbnail of On the origin of the transfer RNA molecule" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" rel="nofollow" href="https://www.academia.edu/123290393/On_the_origin_of_the_transfer_RNA_molecule">On the origin of the transfer RNA molecule</a></div><div class="wp-workCard_item"><span>Journal of Theoretical Biology</span><span>, 1992</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Data and arguments are given in favour of the hypothesis that the primitive tRNA molecule may hav...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Data and arguments are given in favour of the hypothesis that the primitive tRNA molecule may have originated from a direct duplication event involving one of the two halves of the tRNA molecule. It seems that a molecule capable of assuming a hairpin structure was involved as a precursor in this duplication. The two halves of the present tRNAs could, therefore, be considered as paralogous.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290393"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290393"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290393; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=123290393]").text(description); 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="123290391"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/123290391/The_universal_ancestor_was_a_thermophile_or_a_hyperthermophile"><img alt="Research paper thumbnail of The universal ancestor was a thermophile or a hyperthermophile" class="work-thumbnail" src="https://attachments.academia-assets.com/117756789/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/123290391/The_universal_ancestor_was_a_thermophile_or_a_hyperthermophile">The universal ancestor was a thermophile or a hyperthermophile</a></div><div class="wp-workCard_item"><span>Gene</span><span>, 2001</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">By exploiting the correlation between the optimal growth temperature of organisms and a thermophi...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">By exploiting the correlation between the optimal growth temperature of organisms and a thermophily index based on the propensity of amino acids to enter thermophile/hyperthermophile proteins, an analysis is conducted in order to establish whether the last universal common ancestor (LUCA) was a mesophile or a (hyper)thermophile. This objective is reached by using maximum parsimony and maximum likelihood to reconstruct the ancestral sequences of the LUCA for two pairs of sets of paralogous protein sequences by means of the phylogenetic tree topology derived from the small subunit ribosomal RNA, even if this is rooted in all three possible ways. The thermophily index of all the reconstructed ancestral sequences of the LUCA belongs to the set of the thermophile/hyperthermophile sequences, thus supporting the hypotheses that see the LUCA as a thermophile or a hyperthermophile.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="fe7b7a6188acf780e47acb51d7ca811d" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":117756789,"asset_id":123290391,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/117756789/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290391"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290391"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290391; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="123290389"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" rel="nofollow" href="https://www.academia.edu/123290389/Hyperthermophilic_Archaea_as_model_systems_to_study_origin_and_evolution_of_early_organisms"><img alt="Research paper thumbnail of Hyperthermophilic Archaea as model systems to study origin and evolution of early organisms" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" rel="nofollow" href="https://www.academia.edu/123290389/Hyperthermophilic_Archaea_as_model_systems_to_study_origin_and_evolution_of_early_organisms">Hyperthermophilic Archaea as model systems to study origin and evolution of early organisms</a></div><div class="wp-workCard_item"><span>Exo- …</span><span>, 2002</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">The current preponderance of geological and geochemical evidence favours a warm to hot Earth duri...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">The current preponderance of geological and geochemical evidence favours a warm to hot Earth during the first few hundred million years after accretion. Nowadays, volcanic areas, essentially unchanged for at least 4.3 Ga, are populated by hyperthermophilic microorganisms, the ...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290389"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290389"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290389; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=123290389]").text(description); 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</script> <div class="js-work-strip profile--work_container" data-work-id="123290387"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/123290387/The_first_lines_of_divergence_in_the_Bacteria_domain_seem_to_be_the_hyperthermophilic_organisms_a_check_using_an_outgroup_of_sequences_from_mesophiles_in_phylogenetic_analysis"><img alt="Research paper thumbnail of The first lines of divergence in the Bacteria domain seem to be the hyperthermophilic organisms: a check using an outgroup of sequences from mesophiles in phylogenetic analysis" class="work-thumbnail" src="https://attachments.academia-assets.com/117756788/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/123290387/The_first_lines_of_divergence_in_the_Bacteria_domain_seem_to_be_the_hyperthermophilic_organisms_a_check_using_an_outgroup_of_sequences_from_mesophiles_in_phylogenetic_analysis">The first lines of divergence in the Bacteria domain seem to be the hyperthermophilic organisms: a check using an outgroup of sequences from mesophiles in phylogenetic analysis</a></div><div class="wp-workCard_item"><span>Annals of Microbiology</span><span>, 2007</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="62d7701918bab5c4ef11312d6284fc51" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":117756788,"asset_id":123290387,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/117756788/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290387"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290387"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290387; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="123290340"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/123290340/The_extension_reached_by_the_minimization_of_the_polarity_distances_during_the_evolution_of_the_genetic_code"><img alt="Research paper thumbnail of The extension reached by the minimization of the polarity distances during the evolution of the genetic code" class="work-thumbnail" src="https://attachments.academia-assets.com/117756741/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/123290340/The_extension_reached_by_the_minimization_of_the_polarity_distances_during_the_evolution_of_the_genetic_code">The extension reached by the minimization of the polarity distances during the evolution of the genetic code</a></div><div class="wp-workCard_item"><span>Journal of Molecular Evolution</span><span>, 1989</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">The level reached by the optimization of the polarity distances during the evolution of the genet...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">The level reached by the optimization of the polarity distances during the evolution of the genetic code was investigated. The results, although not conclusive, indicate that this optimization level is higher than the data reported in the literature. The results seem compatible with the reaching of an evolutionary minimum, with respect to the optimization of the polarity distances, by the genetic code during its formation.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="347b23868498c9289c9efaa0aaf62f1a" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":117756741,"asset_id":123290340,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/117756741/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="123290340"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="123290340"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 123290340; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=123290340]").text(description); $(".js-view-count[data-work-id=123290340]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 123290340; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='123290340']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="119604158"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/119604158/The_Robust_Statistical_Bases_of_the_Coevolution_Theory_of_Genetic_Code_Origin"><img alt="Research paper thumbnail of The Robust Statistical Bases of the Coevolution Theory of Genetic Code Origin" class="work-thumbnail" src="https://attachments.academia-assets.com/114985394/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/119604158/The_Robust_Statistical_Bases_of_the_Coevolution_Theory_of_Genetic_Code_Origin">The Robust Statistical Bases of the Coevolution Theory of Genetic Code Origin</a></div><div class="wp-workCard_item"><span>Journal of Molecular Evolution</span><span>, 2000</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">A paper (Amirnovin R, J Mol Evol 44:473-476, 1997) seems to undermine the validity of the coevolu...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">A paper (Amirnovin R, J Mol Evol 44:473-476, 1997) seems to undermine the validity of the coevolution theory of genetic code origin by shedding doubt on the connection between the biosynthetic relationships between amino acids and the organization of the genetic code, at a time when the literature on the topic takes this for granted. However, as a few papers cite this paper as evidence against the coevolution theory, and to cast aside all doubt on the subject, we have decided to reanalyze the statistical bases on which this theory is founded. We come to the following conclusions: (1) the methods used in the above referred paper contain certain mistakes, and (2) the statistical foundations on which the coevolution theory is based are extremely robust. We have done this by critically appraising Amirnovin's paper and suggesting an alternative method based on the generation of random codes which, along with the method reported in the literature, allows us to evaluate the significance, in the genetic code, of different sets of amino acid pairs in biosynthetic relationships. In particular, by using this method and after building up a certain set of amino acid pairs reflecting the expectations of the coevolution theory, we show that the presence of this set in the genetic code would be obtained, purely by chance, with a probability of 6 × 10 −5. This observation seems to provide particularly strong support to the coevolution theory.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="dc077dc8ab8bfed32be38be16283d310" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":114985394,"asset_id":119604158,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/114985394/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="119604158"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="119604158"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 119604158; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="119604157"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" rel="nofollow" href="https://www.academia.edu/119604157/On_the_Optimization_of_the_Physicochemical_Distances_between_Amino_Acids_in_the_Evolution_of_the_Genetic_Code"><img alt="Research paper thumbnail of On the Optimization of the Physicochemical Distances between Amino Acids in the Evolution of the Genetic Code" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" rel="nofollow" href="https://www.academia.edu/119604157/On_the_Optimization_of_the_Physicochemical_Distances_between_Amino_Acids_in_the_Evolution_of_the_Genetic_Code">On the Optimization of the Physicochemical Distances between Amino Acids in the Evolution of the Genetic Code</a></div><div class="wp-workCard_item"><span>Journal of Theoretical Biology</span><span>, 1994</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Using the simulated annealing technique we re-examine the role played by the minimization of the ...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Using the simulated annealing technique we re-examine the role played by the minimization of the physicochemical distances between amino acids during the origin of the organization of the genetic code. The results are discussed in the context of the various hypotheses proposed to explain how amino acids were allocated in the genetic code.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="119604157"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="119604157"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 119604157; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=119604157]").text(description); $(".js-view-count[data-work-id=119604157]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 119604157; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='119604157']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); 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</script> <div class="js-work-strip profile--work_container" data-work-id="119604156"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/119604156/The_Historical_Factor_The_Biosynthetic_Relationships_Between_Amino_Acids_and_Their_Physicochemical_Properties_in_the_Origin_of_the_Genetic_Code"><img alt="Research paper thumbnail of The Historical Factor: The Biosynthetic Relationships Between Amino Acids and Their Physicochemical Properties in the Origin of the Genetic Code" class="work-thumbnail" src="https://attachments.academia-assets.com/114985395/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/119604156/The_Historical_Factor_The_Biosynthetic_Relationships_Between_Amino_Acids_and_Their_Physicochemical_Properties_in_the_Origin_of_the_Genetic_Code">The Historical Factor: The Biosynthetic Relationships Between Amino Acids and Their Physicochemical Properties in the Origin of the Genetic Code</a></div><div class="wp-workCard_item"><span>Journal of Molecular Evolution</span><span>, 1998</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Two forces are in general, hypothesized to have influenced the origin of the organization of the ...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Two forces are in general, hypothesized to have influenced the origin of the organization of the genetic code: the physicochemical properties of amino acids and their biosynthetic relationships. In view of this, we have considered a model incorporating these two forces. In particular, we have studied the optimization level of the physicochemical properties of amino acids in the set of amino acid permutation codes that respects the biosynthetic relationships between amino acids. Where the properties of amino acids are represented by polarity and molecular volume we obtain indetermination percentages in the organization of the genetic code of approximately 40%. This indicates that the contingent factor played a significant role in structuring the genetic code. Furthermore, this result is in agreement with the genetic code coevolution hypothesis, which attributes a merely ancillary role to the properties of amino acids while it suggests that it was their biosynthetic relationships that organized the code. Furthermore, this result does not favor the stereochemical models proposed to explain the origin of the genetic code. On the other hand, where the properties of amino acids are represented by polarity alone, we obtain an indetermination percentage of at least 21.5%. This might suggest that the polarity distances played an important role and would therefore provide evidence in favor of the physicochemical hypothesis of genetic code origin. Although, overall, the analysis might have given stronger support to the latter hypothesis, this did not actually occur. The results are therefore discussed in the context of the different theories proposed to explain the origin of the genetic code.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="057b603702684648401abcfa48cdabd3" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":114985395,"asset_id":119604156,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/114985395/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="119604156"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="119604156"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 119604156; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=119604156]").text(description); $(".js-view-count[data-work-id=119604156]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 119604156; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='119604156']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "057b603702684648401abcfa48cdabd3" } } $('.js-work-strip[data-work-id=119604156]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":119604156,"title":"The Historical Factor: The Biosynthetic Relationships Between Amino Acids and Their Physicochemical Properties in the Origin of the Genetic Code","internal_url":"https://www.academia.edu/119604156/The_Historical_Factor_The_Biosynthetic_Relationships_Between_Amino_Acids_and_Their_Physicochemical_Properties_in_the_Origin_of_the_Genetic_Code","owner_id":78314817,"coauthors_can_edit":true,"owner":{"id":78314817,"first_name":"Massimo","middle_initials":null,"last_name":"Di Giulio","page_name":"MassimoDiGiulio","domain_name":"independent","created_at":"2018-03-11T07:50:42.526-07:00","display_name":"Massimo Di Giulio","url":"https://independent.academia.edu/MassimoDiGiulio"},"attachments":[{"id":114985395,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/114985395/thumbnails/1.jpg","file_name":"pl0000634120240520-1-bkwpzs.pdf","download_url":"https://www.academia.edu/attachments/114985395/download_file","bulk_download_file_name":"The_Historical_Factor_The_Biosynthetic_R.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/114985395/pl0000634120240520-1-bkwpzs-libre.pdf?1716187097=\u0026response-content-disposition=attachment%3B+filename%3DThe_Historical_Factor_The_Biosynthetic_R.pdf\u0026Expires=1741332611\u0026Signature=coaxKeAuH75MI~twb4zK6cqGTNi5lecZXJ2Tcrmsy0orPdFzVFXoTzQN5LnaDyOq0xBgAIY18b0N5lTDyUGYwMcADOr4rUUbDy0riHY38ZqSWR0K0jdQV3ZDwLJEzhRL4uy2ZXZ3YlRrOCryXXUkUj3b1AOIVa-2ogOhq5Hd5YB0lgD-mFhyg4ckPKE0MBfSAVaCAKEo8SYwSD8GZGNfj7~jGDr7b2nGOmGxwhujF9CWFIFjc4BuHD6E~D1AWQLUwCnQVJG~y1-yyFAJgE7OGG5rEXw3GMmg0RwWxoLXRip8-kHhDKOd8QEyoVXJQ2BWoNJEohZVyt4~0B06nxFnJw__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="115960029"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/115960029/Some_aspects_of_the_organization_and_evolution_of_the_genetic_code"><img alt="Research paper thumbnail of Some aspects of the organization and evolution of the genetic code" class="work-thumbnail" src="https://attachments.academia-assets.com/112222789/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/115960029/Some_aspects_of_the_organization_and_evolution_of_the_genetic_code">Some aspects of the organization and evolution of the genetic code</a></div><div class="wp-workCard_item"><span>Journal of Molecular Evolution</span><span>, 1989</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">In this paper, I define a measure of the relative position of each amino acid in the genetic code...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">In this paper, I define a measure of the relative position of each amino acid in the genetic code by means of a 21-dimensional vector describing its potential for mutation, in a single step, to each of the other amino acids, or to a chain termination codon. This measure allows us to make a systematic investigation of the type and number of the physicochemical properties of the amino acids that were involved in evolution. The polar character and size of amino acids are identified in this analysis as properties that played a leading role in the evolutionary history of the genetic code. The application of cluster analysis and discriminant analysis reveals the characteristics of the structural organization of the genetic code. Finally, I suggest the existence of a relationship between the molecular weight of the amino acids and the number of synonymous codons.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="b4b1735ab0a7da4d91db430227c87473" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":112222789,"asset_id":115960029,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/112222789/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="115960029"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="115960029"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 115960029; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=115960029]").text(description); $(".js-view-count[data-work-id=115960029]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 115960029; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='115960029']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); 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