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Evolutionary tinkering

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235:; alternatively, the sequence may retain its original identity as an exon or intron, respectively. If an exon that encodes for one or more domains is duplicated, this could directly result in a more complex protein via domain accretion. Eukaryotic genes have undergone frequent internal gene duplication throughout evolutionary history. One example is seen in the dinucleotide-binding regions of glyceraldehyde 3-phosphate dehydrogenase and alcohol dehydrogenase: the duplicated domain is capable of binding with more molecules than the unduplicated. Another is the ovomucoid gene, which is the product of two internal duplications. 254:, gene fusion, or gene fission. Domain shuffling has been found to be at least partially responsible for some traits in modern vertebrates. Most domains only have a small number of uses, while very few domains are used as Lego blocks over and over again in multidomain proteins. Phenotypic innovation does not arise solely from the creation of new proteins, but also from changing gene expression and 114:
materials are at hand to fashion something functional. While the engineer depends on specific materials and tools precisely suited to their project, the tinkerer makes do with miscellaneous scraps and remnants. The resulting creations of the tinkerer emerge from a series of opportunistic events, enriching their repertoire with each encounter.
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each can be employed in multiple ways. According to the tinkering concept, “evolution does not produce novelties from scratch". It comes from previously unseen associations of old materials to modify an existing system to give a new function or combine systems together to enhance the functions. The transformation from
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is the key adaptive feature of humans, yet still holds mysteries regarding its precise purpose. The brain has also evolved through natural selection over millions of years, like other body parts, primarily to serve our reproductive needs. However, the human brain's development was more complex unlike
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is frequently likened to the work of an engineer, yet this analogy falls short. Unlike the engineer who operates based on meticulous planning and a clear vision of the end product, evolution lacks such deliberate intent. Additionally, while the engineer has access to carefully selected materials and
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happens in nature. It explains that evolution works as a tinkerer who experiments with miscellaneous items, unsure of the outcome, and utilizes whatever is available to craft functional objects whose utility may only become evident later. None of the materials serve a defined purpose initially, and
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Cupello, Camila; Hirasawa, Tatsuya; Tatsumi, Norifumi; Yabumoto, Yoshitaka; Gueriau, Pierre; Isogai, Sumio; Matsumoto, Ryoko; Saruwatari, Toshiro; King, Andrew; Hoshino, Masato; Uesugi, Kentaro; Okabe, Masataka; Brito, Paulo M (2022-07-26). Kuraku, Shigehiro; Bronner, Marianne E; Graham, Anthony;
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activities. These older structures lack the discriminative and symbolic abilities of the neocortex and are primarily associated with emotions. Despite the dominance of the neocortex in intellectual processes, the older structures maintain strong connections with automatic centers, ensuring vital
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Moreover, the engineer's creations tend to approach a level of perfection achievable with current technology, whereas evolution does not strive for perfection but rather resembles a tinkerer. This tinkerer, akin to evolution, lacks a precise blueprint of the outcome and instead utilizes whatever
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The process of evolutionary tinkering takes quite a long time. As a meticulous tinkerer who continuously refines its creations, making adjustments, trimming and extending here and there, seizing every chance to gradually tailor them to their evolving purposes, this process happens over countless
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functions like obtaining food and responding to threats. This evolutionary process, characterized by the emergence of a dominant neocortex alongside the persistence of older systems, resembles a tinkering process, where new elements are added onto existing ones without fully replacing them.
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illustrates a process akin to tinkering rather than deliberate engineering. It originated in certain freshwater fish faced with oxygen deficient environments, leading them to ingest air and absorb oxygen through their esophageal walls. Over time, this behavior favored the enlargement of the
308:. Although they are too rare to notably increase the number of proteins in a given lineage, the tinkering model posits that adding just a few Lego blocks to the collection allows for many new possible combinations of domains, i.e., proteins with new shapes and functions. 222:
There are several forms of gene duplication. The product of whole-gene duplication is two copies of the gene, whereas that of diploid-type gene duplication is one gene that has doubled in length. Internal gene duplication results in repeated
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first introduced the idea of tinkering to a broad audience of scientists, drawing from diverse fields such as molecular biology, evolutionary biology, and cultural anthropology. The concept of tinkering, or more precisely, the notion of
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by joining two genes together) and gene fission or fragmentation, which results in splitting one gene with many domains into multiple smaller genes, are the other two molecular mechanisms by which mosaic proteins can be formed.
171:, combination, and reassorting these original sequences. It is well established that gene duplication has produced a great deal of diversity throughout evolutionary history. One example of molecular tinkering can be found in 83:, serves as a theoretical framework for analyzing various phenomena characterized by a common underlying process: the opportunistic rearrangement and recombination of existing elements. Jacob and Monad also won the 201:
to explain: the domains can be taken apart and put together again in unique ways, thus changing the shape and function of the protein. There are many different means by which tinkering can result in molecular and
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Kawashima, Takeshi; Kawashima, Shuichi; Tanaka, Chisaki; Murai, Miho; Yoneda, Masahiko; Putnam, Nicholas H.; Rokhsar, Daniel S.; Kanehisa, Minoru; Satoh, Nori; Wada, Hiroshi (May 14, 2009).
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sequences within a gene, and less than 100% of the gene is replicated. Because adding nucleotides to a sequence could impact splicing, this process may result in changing the identity of
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novelty, primarily by taking apart the Lego blocks of proteins and putting them together again in unique patterns. Generally, these processes add to the organizational complexity of the
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is a very rare phenomenon in which an intron becomes an exon. In pseudoexonization, an exon becomes nonfunctional; this in turn changes the shape and function of the protein.
138:, onto older ones. This rapid evolution led to a division between the neocortex, responsible for intellectual functions, and the older structures, controlling 277:
is another mechanism of molecular tinkering that may be responsible for increasing diversity in the proteome. One special kind of alternative splicing is
281:, which produce intron-encoded proteins. It has been proposed that nested gene structures could be maintained via neutral processes according to the 1698: 960: 855: 282: 84: 126:
esophageal surface area, eventually giving rise to lung-like structures through the emergence and enlargement of esophageal diverticula.
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disappear, it is possible for genes to be lost via one of two mechanisms. The first is deleting a single-copy gene. The second is
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anatomical structures, and is uncommon due to its often deleterious nature. In the rare case that gene loss becomes fixed in a
1642: 1717: 1493: 1460: 182:; in this case, the tinkerer used whatever tools were at her disposal, including materials from an entirely different 134:
straightforward evolutionary changes such as a leg into a wing. It involved adding new structures, particularly the
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is profoundly inefficient, despite the fact that it catalyzes one of the most important reactions on the planet:
1586: 1523: 1498: 1381: 1301: 1571: 1455: 1424: 1325: 32: 1096: 1682: 1576: 1503: 1402: 1340: 1335: 1266: 1201: 1032:"Processes of fungal proteome evolution and gain of function: gene duplication and domain rearrangement" 936: 296:
is very rare. The most probable path from noncoding DNA to a protein-coding gene is to first become a
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that has a defined shape, which determines the function of the protein. Some have used the analogy of
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of the earliest organisms were very short, and all subsequent genes were formed by
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Jacob was convinced that although morphological analysis supports his notion of
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when the atmospheric conditions were drastically different than they are today.
1186: 258:. One example of novelty associated with domain shuffling is multicellularity. 1630: 1330: 1283: 913: 847: 646: 344: 336: 301: 297: 224: 122: 88: 35:
during evolution is such an event which has elaborated the existing function.
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Grunberg-Manago, Marianne; Clark, Brian F. C.; Zachau, Hans G., eds. (1989).
822: 772: 715: 655: 581: 458: 435:"Using Old Stuff in New Ways: Innovation as a Case of Evolutionary Tinkering" 403: 189:
To understand molecular tinkering, it is important to grasp the concept of a
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Koonin, Eugene V; Aravind, L; Kondrashov, Alexey S (June 9, 2000).
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Most of the time, traits in nature are barely favorable enough for
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Graur, Dan (2016). "Chapter 8: Evolution by Molecular Tinkering".
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Cohen-Gihon, Inbar; Sharan, Roded; Nussinov, Ruth (2011-06-01).
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Graur, Dan (2016). "Chapter 7: Evolution by DNA Duplication".
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De novo evolution of protein-coding genes from non-coding DNA
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relies on the resources available in its surroundings.
898:"Evolutionary tinkering with mitochondrial nucleoids" 339:, which has no functional paralogs, is comparable to 312:
Exonization of introns and pseudoexonization of exons
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Kucej, Martin; Butow, Ronald A. (December 1, 2007).
1675: 1604: 1532: 1486: 1479: 1443: 1395: 1359: 1292: 1229: 1136:"Domain shuffling and the evolution of vertebrates" 159:, one would find more evidence of tinkering at the 74:In his seminal article 'Evolution and Tinkering', 749:"Psychosomatic Disease and the "Visceral Brain"" 106:specialized equipment tailored for their tasks, 335:of a single-copy gene; this produces a unitary 300:, similar to how functional genes first become 1202: 935:Das, Sudeshna; Smith, Temple F (2000-01-01), 433:Sanger, Mary Bryna; Levin, Martin A. (1992). 163:level. The tinkering model suggests that the 8: 799:"François Jacob: Bricolage and the Possible" 1483: 1209: 1195: 1187: 1167: 1071: 1006: 839:Evolutionary Tinkering in Gene Expression 723: 705: 663: 645: 439:Journal of Policy Analysis and Management 937:"Identifying nature's protein lego set" 355: 1699:Index of evolutionary biology articles 609:. New York, Boston: H.M. 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(November 1949). 606:Origin of species / Charles Darwin 193:, which is a distinct region of a 14: 634:Life Sciences, Society and Policy 323:Gene loss and unitary pseudogenes 1466:Evolution of sexual reproduction 765:10.1097/00006842-194911000-00003 151:Evolution by molecular tinkering 261:Gene fusion (the creation of a 178:, some of which originate from 1237:Genotype–phenotype distinction 873:Molecular and Genome Evolution 548:Morange, Michel (2013-05-23). 525:Molecular and Genome Evolution 1: 1494:Regulation of gene expression 1008:10.1016/S0092-8674(00)80867-3 953:10.1016/S0065-3233(00)54006-6 941:Advances in Protein Chemistry 797:Marks, John (December 2020). 1664:Endless Forms Most Beautiful 1444:Evolution of genetic systems 1252:Gene–environment correlation 1247:Gene–environment interaction 1056:10.1088/1478-3975/8/3/035009 550:"François Jacob (1920–2013)" 256:protein-protein interactions 98:Engineering versus tinkering 87:in 1965 for his work on the 54:. This is likely due to the 1643:Christiane NĂĽsslein-Volhard 947:, Academic Press: 159–183, 304:before becoming completely 283:neutral theory of evolution 1739: 1519:Hedgehog signaling pathway 1396:Developmental architecture 1095:Letunic, I. (2002-06-15). 46:to survive. For instance, 1696: 1346:Transgressive segregation 914:10.1016/j.tcb.2007.08.007 848:10.1007/978-1-4684-5664-6 803:Nottingham French Studies 647:10.1186/s40504-018-0086-x 372:"Evolution and Tinkering" 218:Internal gene duplication 22:is an explanation of how 1101:Human Molecular Genetics 603:Darwin, Charles (1900). 370:Jacob, François (1977). 1524:Notch signaling pathway 1499:Gene regulatory network 1382:Dual inheritance theory 1572:cis-regulatory element 1480:Control of development 1360:Non-genetic influences 1326:evolutionary landscape 1113:10.1093/hmg/11.13.1561 902:Trends in Cell Biology 753:Psychosomatic Medicine 396:10.1126/science.860134 20:Evolutionary tinkering 1683:Nature versus nurture 1587:Cell surface receptor 1504:Evo-devo gene toolkit 1403:Developmental biology 1341:Polygenic inheritance 1267:Quantitative genetics 1152:10.1101/gr.087072.108 815:10.3366/nfs.2020.0294 688:Long, John A (eds.). 615:10.5962/bhl.title.959 329:selective constraints 1718:Biological evolution 1592:Transcription factor 1307:Genetic assimilation 1294:Genetic architecture 333:nonfunctionalization 275:Alternative splicing 270:Alternative splicing 1688:Morphogenetic field 1605:Influential figures 1048:2011PhBio...8c5009C 707:10.7554/eLife.77156 566:2013Natur.497..440M 388:1977Sci...196.1161J 382:(4295): 1161–1166. 117:The development of 58:originating in the 1377:Genomic imprinting 294:De novo gene birth 16:Concept in biology 1705: 1704: 1638:Eric F. Wieschaus 1600: 1599: 1418:Pattern formation 1322:Fitness landscape 1107:(13): 1561–1567. 962:978-0-12-034254-9 857:978-1-4684-5666-0 103:Natural selection 1730: 1723:Biology theories 1648:William McGinnis 1617:Richard Lewontin 1612:C. H. Waddington 1484: 1461:Neutral networks 1211: 1204: 1197: 1188: 1182: 1181: 1171: 1146:(8): 1393–1403. 1131: 1125: 1124: 1092: 1086: 1085: 1075: 1036:Physical Biology 1027: 1021: 1020: 1010: 986: 980: 979: 978: 977: 932: 926: 925: 893: 887: 886: 868: 862: 861: 833: 827: 826: 794: 785: 784: 744: 738: 737: 727: 709: 684: 678: 677: 667: 649: 625: 619: 618: 600: 594: 593: 545: 539: 538: 520: 471: 470: 430: 424: 423: 367: 184:taxonomic domain 1738: 1737: 1733: 1732: 1731: 1729: 1728: 1727: 1708: 1707: 1706: 1701: 1692: 1671: 1658:Sean B. Carroll 1596: 1528: 1475: 1439: 1391: 1372:Maternal effect 1355: 1288: 1225: 1215: 1185: 1140:Genome Research 1133: 1132: 1128: 1094: 1093: 1089: 1029: 1028: 1024: 988: 987: 983: 975: 973: 963: 934: 933: 929: 908:(12): 586–592. 895: 894: 890: 883: 870: 869: 865: 858: 835: 834: 830: 796: 795: 788: 746: 745: 741: 686: 685: 681: 627: 626: 622: 602: 601: 597: 574:10.1038/497440a 547: 546: 542: 535: 522: 521: 474: 451:10.2307/3325134 432: 431: 427: 369: 368: 357: 353: 325: 314: 291: 272: 246:are encoded by 244:Mosaic proteins 241: 239:Mosaic proteins 220: 153: 121:in terrestrial 100: 72: 60:common ancestor 52:carbon fixation 17: 12: 11: 5: 1736: 1734: 1726: 1725: 1720: 1710: 1709: 1703: 1702: 1697: 1694: 1693: 1691: 1690: 1685: 1679: 1677: 1673: 1672: 1670: 1669: 1668: 1667: 1655: 1650: 1645: 1640: 1635: 1634: 1633: 1622:François Jacob 1619: 1614: 1608: 1606: 1602: 1601: 1598: 1597: 1595: 1594: 1589: 1584: 1579: 1574: 1569: 1564: 1559: 1558: 1557: 1547: 1542: 1536: 1534: 1530: 1529: 1527: 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756: 752: 742: 697: 693: 682: 637: 633: 623: 605: 598: 557: 553: 543: 524: 442: 438: 428: 379: 375: 326: 315: 292: 279:nested genes 273: 260: 242: 221: 188: 156: 154: 128: 116: 112: 101: 89: 80: 73: 41: 37: 19: 18: 1653:Mike Levine 1562:Distal-less 1387:Polyphenism 1367:Epigenetics 1219:development 317:Exonization 302:pseudogenes 263:fusion gene 214:, or both. 199:Lego blocks 169:duplication 123:vertebrates 85:Nobel Prize 29:unicellular 1712:Categories 1631:Lac operon 1456:Robustness 1435:Modularity 1430:Metamerism 1336:Plasticity 1331:Pleiotropy 1284:Heterotopy 976:2024-05-08 700:: e77156. 351:References 345:population 337:pseudogene 225:nucleotide 204:phenotypic 180:eukaryotes 1582:Morphogen 1567:Engrailed 1550:Pax genes 1471:Tinkering 1317:Epistasis 1312:Dominance 1223:phenotype 1160:1088-9051 1064:1478-3975 823:0029-4586 773:0033-3174 716:2050-084X 656:2195-7819 640:(1): 18. 582:0028-0836 459:0276-8739 404:0036-8075 341:vestigial 298:protogene 161:molecular 157:bricolage 140:emotional 136:neocortex 108:evolution 81:bricolage 44:organisms 24:evolution 1545:Hox gene 1533:Elements 1514:Homeobox 1178:19443856 1121:12045209 1082:21572172 1017:10892642 971:10829228 922:17981466 781:15410445 734:35880746 674:30099657 590:23698437 306:nongenic 212:proteome 144:visceral 64:plastids 1676:Debates 1487:Systems 1413:Eyespot 1277:Neoteny 1169:2720177 1073:3140765 1044:Bibcode 725:9323002 665:6087506 562:Bibcode 467:3325134 412:1744610 384:Bibcode 376:Science 229:introns 195:protein 62:of all 48:RuBisCO 1577:Ligand 1257:Operon 1176:  1166:  1158:  1119:  1080:  1070:  1062:  1015:  969:  959:  920:  879:  854:  821:  779:  771:  732:  722:  714:  672:  662:  654:  588:  580:  554:Nature 531:  465:  457:  420:860134 418:  410:  402:  210:, the 208:genome 92:operon 56:enzyme 39:eons. 694:eLife 463:JSTOR 408:JSTOR 327:When 233:exons 165:genes 131:brain 119:lungs 1217:The 1174:PMID 1156:ISSN 1117:PMID 1078:PMID 1060:ISSN 1013:PMID 995:Cell 967:PMID 957:ISBN 918:PMID 877:ISBN 852:ISBN 819:ISSN 777:PMID 769:ISSN 730:PMID 712:ISSN 670:PMID 652:ISSN 586:PMID 578:ISSN 529:ISBN 455:ISSN 416:PMID 400:ISSN 231:and 142:and 129:The 1221:of 1164:PMC 1148:doi 1109:doi 1068:PMC 1052:doi 1003:doi 999:101 949:doi 910:doi 844:doi 811:doi 761:doi 720:PMC 702:doi 660:PMC 642:doi 611:doi 570:doi 558:497 447:doi 392:doi 380:196 90:lac 31:to 1714:: 1624:+ 1172:. 1162:. 1154:. 1144:19 1142:. 1138:. 1115:. 1105:11 1103:. 1099:. 1076:. 1066:. 1058:. 1050:. 1038:. 1034:. 1011:. 997:. 993:. 965:, 955:, 945:54 939:, 916:. 906:17 904:. 900:. 850:. 842:. 817:. 807:59 805:. 801:. 789:^ 775:. 767:. 757:11 755:. 751:. 728:. 718:. 710:. 698:11 696:. 692:. 668:. 658:. 650:. 638:14 636:. 632:. 584:. 576:. 568:. 556:. 552:. 475:^ 461:. 453:. 443:11 441:. 437:. 414:. 406:. 398:. 390:. 378:. 374:. 358:^ 285:. 186:. 94:. 1324:/ 1210:e 1203:t 1196:v 1180:. 1150:: 1123:. 1111:: 1084:. 1054:: 1046:: 1040:8 1019:. 1005:: 951:: 924:. 912:: 885:. 860:. 846:: 825:. 813:: 783:. 763:: 736:. 704:: 676:. 644:: 617:. 613:: 592:. 572:: 564:: 537:. 469:. 449:: 422:. 394:: 386::

Index

evolution
unicellular
multicellular
organisms
RuBisCO
carbon fixation
enzyme
common ancestor
plastids
François Jacob
Nobel Prize
lac operon
Natural selection
evolution
lungs
vertebrates
brain
neocortex
emotional
visceral
molecular
genes
duplication
mitochondrial
nucleoproteins
eukaryotes
taxonomic domain
protein domain
protein
Lego blocks

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