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The reaction consists in an aldolization-type C,C-bond formation, accompanied by a (presumably aldehyde-catalyzed) hydration of one of the two nitrile groups and the formation of two cyclic aminal-type groupings, each of the latter incorporating an additional molecule of the aldehyde. 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Various aldehydes react with glycine to give corresponding hydroxyalkyl amino acids, which on reduction with formic acid are converted to reduced amino acids. Formaldehyde reacts with uracil to give 5-hydroxymethyl uracil which on reduction with formic acid yields thymine. Pyrrole formed by heating serine reacts with aldehydes to form porphyrins. Clays do not seem to influence most of these reactions, except the uracil-formaldehyde — formic acid reaction which results in enhanced yield of thymine.", "tags": [], "relations": {}, "dateAdded": "2011-02-08T12:44:07Z", "dateModified": "2011-02-08T12:44:07Z" } }, { "key": "PXU365TJ", "version": 1, "library": { "type": "group", "id": 32667, "name": "prebiotic-chemistry", "links": { "alternate": { "href": "https://www.zotero.org/groups/prebiotic-chemistry", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/32667/items/PXU365TJ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/prebiotic-chemistry/items/PXU365TJ", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/32667/items/R5EXJQ6D", "type": "application/json" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { "href": "https://www.zotero.org/mark-doerr", "type": "text/html" } } } }, "data": { "key": "PXU365TJ", "version": 1, "parentItem": "R5EXJQ6D", "itemType": "attachment", "linkMode": "linked_url", "title": "BF00926938", "accessDate": "2011-01-17T13:45:47Z", "url": "http://dx.doi.org/10.1007/BF00926938", "note": "", "contentType": "", "charset": "", "tags": [], "relations": {}, "dateAdded": "2011-02-08T12:44:07Z", "dateModified": "2011-02-08T12:44:07Z" } }, { "key": "3ZQXT7JS", "version": 1, "library": { "type": "group", "id": 32667, "name": "prebiotic-chemistry", "links": { "alternate": { "href": "https://www.zotero.org/groups/prebiotic-chemistry", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/32667/items/3ZQXT7JS", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/prebiotic-chemistry/items/3ZQXT7JS", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/32667/items/R5EXJQ6D", "type": "application/json" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { "href": "https://www.zotero.org/mark-doerr", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "3ZQXT7JS", "version": 1, "parentItem": "R5EXJQ6D", "itemType": "note", "note": "Biopolymers are formed by dehydration-type condensation reactions. In aqueous solutions dehydration reactions are very unlikely to happen spontaneously. However, coupling of dehydration-condensation to the hydrolysis of condensing agents could facilitate the synthesis of biopolymers in an aqueous solution. The literature shows that the peptides, nucleosides, nucleotides and oligonucleotides can be formed in this way. A careful study of the literature pertaining to prebiotic condensing agents was conducted in order to determine the most plausible prebiotic synthesis of biopolymers. The condensing agents taken into consideration are cyanamide, carbodiimide, dicyanamide, dicyandiamide, hydrogec-cyanide-tetramer, cyanogen and the linear- and cyclic polyphosphates. From both a chemical as well as biological point of view the polyphosphates appear to be the most plausible general prebiotic condensing agent.", "tags": [], "relations": {}, "dateAdded": "2011-02-08T12:44:07Z", "dateModified": "2011-02-08T12:44:07Z" } }, { "key": "WM49RUQK", "version": 1, "library": { "type": "group", "id": 32667, "name": "prebiotic-chemistry", "links": { "alternate": { "href": "https://www.zotero.org/groups/prebiotic-chemistry", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/32667/items/WM49RUQK", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/prebiotic-chemistry/items/WM49RUQK", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/32667/items/NJENAGNR", "type": "application/json" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { "href": "https://www.zotero.org/mark-doerr", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "WM49RUQK", "version": 1, "parentItem": "NJENAGNR", "itemType": "note", "note": "The claim by Nelson et al. (2001) that the reactionof cyanoacetaldehyde and urea provides `an efficient prebioticsynthesis' of cytosine is disputed. The authors have not dealt withthe important points presented in a criticism of this reaction(Shapiro, 1999): (1) The reactants undergo side reactions with commonnucleophiles that appear to proceed more rapidly than cytosineformation, and (2) No reactions have been described thus far thatwould produce cytosine at a rate sufficient to compensate for itsdecomposition by deamination, and permit accumulation over extendedperiods of time. Instead, Nelson et al. have conducted `drying-down' experiments, inan effort to simulate evaporations on the early Earth, but thedesign of these experiments is flawed. The initial reactantconcentrations are much higher than might be expected in a naturalsetting, and potentially interfering substances such as glycine,cyanide and thiols have been excluded. `Drying beaches and dryinglagoons' have been invoked as sites for such a reaction but noeffort has been made to describe the characteristics of such sitesor to estimate their frequency with reference to the present Earth.In the absence of contradictory data, the conclusion put forward inShapiro (1999) remains valid: `It was quite unlikely that cytosineplayed a role in the origin of life'.", "tags": [], "relations": {}, "dateAdded": "2011-02-08T12:44:07Z", "dateModified": "2011-02-08T12:44:07Z" } }, { "key": "2QJ2M23T", "version": 1, "library": { "type": "group", "id": 32667, "name": "prebiotic-chemistry", "links": { "alternate": { "href": "https://www.zotero.org/groups/prebiotic-chemistry", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/32667/items/2QJ2M23T", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/prebiotic-chemistry/items/2QJ2M23T", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/32667/items/8EB9XAPD", "type": "application/json" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { "href": "https://www.zotero.org/mark-doerr", "type": "text/html" } } } }, "data": { "key": "2QJ2M23T", "version": 1, "parentItem": "8EB9XAPD", "itemType": "attachment", "linkMode": "linked_url", "title": "BF01808312", "accessDate": "2011-01-17T13:52:58Z", "url": "http://dx.doi.org/10.1007/BF01808312", "note": "", "contentType": "", "charset": "", "tags": [], "relations": {}, "dateAdded": "2011-02-08T12:44:07Z", "dateModified": "2011-02-08T12:44:07Z" } }, { "key": "35P86FX8", "version": 1, "library": { "type": "group", "id": 32667, "name": "prebiotic-chemistry", "links": { "alternate": { "href": "https://www.zotero.org/groups/prebiotic-chemistry", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/32667/items/35P86FX8", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/prebiotic-chemistry/items/35P86FX8", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/32667/items/8EB9XAPD", "type": "application/json" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { "href": "https://www.zotero.org/mark-doerr", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "35P86FX8", "version": 1, "parentItem": "8EB9XAPD", "itemType": "note", "note": "In the presence of a base such as ammonia liquid HCN (bp 25 °C) polymerizes readily to a black solid from which a yellow-brown powder can be extracted by water and further hydrolyzed to yielda-amino acids. These macromolecules could be major components of the dark matter observed on many bodies in the outer solar system. The non-volatile black crust of comet Halley, for example, may consist largely of such polymers, since the original presence on cometary nuclei of frozen volatiles such as methane, ammonia, and water makes them possible sites for the formation and condensed-phase polymerization of hydrogen cyanide. It seems likely, too, that HCN polymers are among the dark —C=N bearing solids identified spectroscopically by Cruikshanket al. in the dust of some other comets, on the surfaces of several asteroids of spectral class D, within the rings of Uranus, and covering the dark hemisphere of Saturn's satellite Iapetus. HCN polymerization could account also for the yellow-orange-brown coloration of Jupiter and Saturn, as well as for the orange haze high in Titan's atmosphere. Implications for prebiotic chemistry are profound. Primitive Earth may have been covered by HCN polymers through cometary bombardment or terrestrial synthesis, producing a proteinaceous matrix that promoted the molecular interactions leading to the emergence of life.", "tags": [], "relations": {}, "dateAdded": "2011-02-08T12:44:07Z", "dateModified": "2011-02-08T12:44:07Z" } }, { "key": "BETXC6DF", "version": 1, "library": { "type": "group", "id": 32667, "name": "prebiotic-chemistry", "links": { "alternate": { "href": "https://www.zotero.org/groups/prebiotic-chemistry", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/32667/items/BETXC6DF", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/prebiotic-chemistry/items/BETXC6DF", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/32667/items/FP7MP6KP", "type": "application/json" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { 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"section": "", "partNumber": "", "partTitle": "", "pages": "241-262", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://dx.doi.org/10.1007/BF02627944", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0169-6149", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "0242", "rights": "", "extra": "10.1007/BF02627944", "tags": [], "collections": [ "FUVBGZ7J" ], "relations": {}, "dateAdded": "2010-12-02T12:29:40Z", "dateModified": "2010-12-02T12:29:54Z" } }, { "key": "XS78RNK2", "version": 1, "library": { "type": "group", "id": 32667, "name": "prebiotic-chemistry", "links": { "alternate": { "href": "https://www.zotero.org/groups/prebiotic-chemistry", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/32667/items/XS78RNK2", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/prebiotic-chemistry/items/XS78RNK2", "type": "text/html" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { "href": "https://www.zotero.org/mark-doerr", "type": "text/html" } } }, "creatorSummary": "Eigen and Winkler-Oswatitsch", "parsedDate": "1981", "numChildren": 2 }, "data": { "key": "XS78RNK2", "version": 1, "itemType": "journalArticle", "title": "Transfer-RNA: The early adaptor", "creators": [ { "creatorType": "author", "firstName": "Manfred", "lastName": "Eigen" }, { "creatorType": "author", "firstName": "Ruthild", "lastName": "Winkler-Oswatitsch" } ], "abstractNote": "Evolutionary history of tRNA is studied by comparative sequence analysis of two specified tRNA's at various phylogenetic levels and of tRNA families within four different species. Criteria are developed that allow 1) to distinguish between convergent and divergent evolution, 2) to determine the mechanism of divergence and 3) to estimate the degree of randomization of the variable parts of the sequences. The conclusion of these investigations is that tRNA's represent ancient molecules that existed in the form of a mutant distribution prior to their integration into genomes.", "publicationTitle": "Naturwissenschaften", "publisher": "", "place": "", "date": "1981", "volume": "68", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "217-228", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://dx.doi.org/10.1007/BF01047323", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0028-1042", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "0110", "rights": "", "extra": "10.1007/BF01047323", "tags": [], "collections": [ "FUVBGZ7J" ], "relations": {}, "dateAdded": "2010-12-02T12:29:40Z", "dateModified": "2010-12-02T12:29:53Z" } }, { "key": "8KF994VR", "version": 1, "library": { "type": "group", "id": 32667, "name": "prebiotic-chemistry", "links": { "alternate": { "href": "https://www.zotero.org/groups/prebiotic-chemistry", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/32667/items/8KF994VR", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/prebiotic-chemistry/items/8KF994VR", "type": "text/html" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { "href": "https://www.zotero.org/mark-doerr", "type": "text/html" } } }, "creatorSummary": "Eigen and Winkler-Oswatitsch", "parsedDate": "1981", "numChildren": 2 }, "data": { "key": "8KF994VR", "version": 1, "itemType": "journalArticle", "title": "Transfer-RNA, an early gene?", "creators": [ { "creatorType": "author", "firstName": "Manfred", "lastName": "Eigen" }, { "creatorType": "author", "firstName": "Ruthild", "lastName": "Winkler-Oswatitsch" } ], "abstractNote": "The theory of self-reproductive molecular systems involves the consequence that translation must have started from a selected distribution of RNA molecules, that comprised GC-rich sequences of a length < 100 nucleotides. This implies a joint function of messenger and adaptor, which both had to be recruited from the same mutant distribution. The reconstruction of tRNA precursors yields such a molecule showing some reverberation of a codon pattern GNC. These findings suggest that tRNA has been the earliest component of the translation machinery.", "publicationTitle": "Naturwissenschaften", "publisher": "", "place": "", "date": "1981", "volume": "68", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "282-292", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://dx.doi.org/10.1007/BF01047470", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0028-1042", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "0103", "rights": "", "extra": "10.1007/BF01047470", "tags": [], "collections": [ "FUVBGZ7J" ], "relations": {}, "dateAdded": "2010-12-02T12:29:40Z", "dateModified": "2010-12-02T12:29:52Z" } }, { "key": "ITTBI5KE", "version": 1, "library": { "type": "group", "id": 32667, "name": "prebiotic-chemistry", "links": { "alternate": { "href": "https://www.zotero.org/groups/prebiotic-chemistry", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/32667/items/ITTBI5KE", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/prebiotic-chemistry/items/ITTBI5KE", "type": "text/html" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { "href": "https://www.zotero.org/mark-doerr", "type": "text/html" } } }, "creatorSummary": "Eigen and Schuster", "parsedDate": "1978-07-01", "numChildren": 2 }, "data": { "key": "ITTBI5KE", "version": 1, "itemType": "journalArticle", "title": "The Hypercycle", "creators": [ { "creatorType": "author", "firstName": "Manfred", "lastName": "Eigen" }, { "creatorType": "author", "firstName": "Peter", "lastName": "Schuster" } ], "abstractNote": "", "publicationTitle": "Naturwissenschaften", "publisher": "", "place": "", "date": "1978-07-01", "volume": "65", "issue": "7", "section": "", "partNumber": "", "partTitle": "", "pages": "341-369-369", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://dx.doi.org/10.1007/BF00439699", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0028-1042", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "0497", "rights": "", "extra": "", "tags": [ { "tag": "Biomedical and Life Sciences" } ], "collections": [ "FUVBGZ7J" ], "relations": {}, "dateAdded": "2010-12-02T12:29:40Z", "dateModified": "2010-12-02T12:29:51Z" } }, { "key": "BU5JMZ7V", "version": 1, "library": { "type": "group", "id": 32667, "name": "prebiotic-chemistry", "links": { "alternate": { "href": "https://www.zotero.org/groups/prebiotic-chemistry", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/32667/items/BU5JMZ7V", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/prebiotic-chemistry/items/BU5JMZ7V", "type": "text/html" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { "href": "https://www.zotero.org/mark-doerr", "type": "text/html" } } }, "creatorSummary": "Eigen and Schuster", "parsedDate": "1978", "numChildren": 0 }, "data": { "key": "BU5JMZ7V", "version": 1, "itemType": "journalArticle", "title": "The Hypercycle", "creators": [ { "creatorType": "author", "firstName": "Manfred", "lastName": "Eigen" }, { "creatorType": "author", "firstName": "Peter", "lastName": "Schuster" } ], "abstractNote": "The proposed model for a ‘realistic hypercycle’ is closely associated with the molecular organization of a primitive replication and translation apparatus. Hypercyclic organization offers selective stabilization and evolutive adaptation for all geno- and phenotypic constituents of the functionally linked ensemble. It originates in a molecular quasi-species and evolves by way of mutation and gene duplication to greater complexity. Its early structure appears to be reflected in: the assignment of codons to amino acids, in sequence homologies of tRNAs, in dual enzymic functions of replication and translation, and in the structural and functional organization of the genome of the prokaryotic cell.", "publicationTitle": "Naturwissenschaften", "publisher": "", "place": "", "date": "1978", "volume": "65", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "341-369", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://dx.doi.org/10.1007/BF00439699", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0028-1042", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "0497", "rights": "", "extra": "10.1007/BF00439699", "tags": [], "collections": [ "FUVBGZ7J" ], "relations": {}, "dateAdded": "2010-12-02T12:29:40Z", "dateModified": "2010-12-02T12:29:50Z" } } ]