BIO-complexity最新文献_第5页

The Limits of Complex Adaptation: An Analysis Based on a Simple Model of Structured Bacterial Populations 复杂适应的极限:基于结构细菌种群简单模型的分析

BIO-complexity Pub Date : 2010-12-21 DOI: 10.5048/BIO-C.2010.4

D. Axe

{"title":"The Limits of Complex Adaptation: An Analysis Based on a Simple Model of Structured Bacterial Populations","authors":"D. Axe","doi":"10.5048/BIO-C.2010.4","DOIUrl":"https://doi.org/10.5048/BIO-C.2010.4","url":null,"abstract":"To explain life's current level of complexity, we must first explain genetic innovation. Recognition of this fact has generated interest in the evolutionary feasibility of complex adaptations--adaptations requiring multiple mutations, with all intermediates being non-adaptive. Intuitively, one expects the waiting time for arrival and fixation of these adaptations to have exponential dependence on d , the number of specific base changes they require. Counter to this expectation, Lynch and Abegg have recently concluded that in the case of selectively neutral intermediates, the waiting time becomes independent of d as d becomes large. Here, I confirm the intuitive expectation by showing where the analysis of Lynch and Abegg erred and by developing new treatments of the two cases of complex adaptation--the case where intermediates are selectively maladaptive and the case where they are selectively neutral. In particular, I use an explicit model of a structured bacterial population, similar to the island model of Maruyama and Kimura, to examine the limits on complex adaptations during the evolution of paralogous genes--genes related by duplication of an ancestral gene. Although substantial functional innovation is thought to be possible within paralogous families, the tight limits on the value of d found here ( d ≤ 2 for the maladaptive case, and d ≤ 6 for the neutral case) mean that the mutational jumps in this process cannot have been very large. Whether the functional divergence commonly attributed to paralogs is feasible within such tight limits is far from certain, judging by various experimental attempts to interconvert the functions of supposed paralogs. This study provides a mathematical framework for interpreting experiments of that kind, more of which will needed before the limits to functional divergence become clear.","PeriodicalId":89660,"journal":{"name":"BIO-complexity","volume":"2010 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2010-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70593690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 16

A Vivisection of the ev Computer Organism: Identifying Sources of Active Information 计算机有机体的活体解剖:识别活动信息的来源

BIO-complexity Pub Date : 2010-12-15 DOI: 10.5048/BIO-C.2010.3

George D. Montañez, W. Ewert, W. Dembski, R. Marks

引用次数: 15

Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness 简化进化可以阻止种群采取简单的适应路径来获得高适应性

BIO-complexity Pub Date : 2010-04-30 DOI: 10.5048/BIO-C.2010.2

A. Gauger, S. Ebnet, P. F. Fahey, R. Seelke

{"title":"Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness","authors":"A. Gauger, S. Ebnet, P. F. Fahey, R. Seelke","doi":"10.5048/BIO-C.2010.2","DOIUrl":"https://doi.org/10.5048/BIO-C.2010.2","url":null,"abstract":"New functions requiring multiple mutations are thought to be evolutionarily feasible if they can be achieved by means of adaptive paths-successions of simple adaptations each involving a single mutation. The presence or absence of these adaptive paths to new function therefore constrains what can evolve. But since emerging functions may require costly over-expression to improve fitness, it is also possible for reductive (i.e., cost-cutting) mutations that eliminate over-expression to be adaptive. Consequently, the relative abundance of these kinds of adaptive paths--constructive paths leading to new function versus reductive paths that increase metabolic efficiency--is an important evolutionary constraint. To study the impact of this constraint, we observed the paths actually taken during long-term laboratory evolution of an Escherichia coli strain carrying a doubly mutated trpA gene. The presence of these two mutations prevents tryptophan biosynthesis. One of the mutations is partially inactivating, while the other is fully inactivating, thus permitting a two-step adaptive path to full tryptophan biosynthesis. Despite the theoretical existence of this short adaptive path to high fitness, multiple independent lines grown in tryptophan-limiting liquid culture failed to take it. Instead, cells consistently acquired mutations that reduced expression of the double-mutant trpA gene. Our results show that competition between reductive and constructive paths may significantly decrease the likelihood that a particular constructive path will be taken. This finding has particular significance for models of gene recruitment, since weak new functions are likely to require costly over-expression in order to improve fitness. If reductive, cost-cutting mutations are more abundant than mutations that convert or improve function, recruitment may be unlikely even in cases where a short adaptive path to a new function exists.","PeriodicalId":89660,"journal":{"name":"BIO-complexity","volume":"2010 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2010-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70593502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 15

The Case Against a Darwinian Origin of Protein Folds 反对蛋白质折叠的达尔文起源论的案例

BIO-complexity Pub Date : 2010-04-15 DOI: 10.5048/BIO-C.2010.1

D. Axe

{"title":"The Case Against a Darwinian Origin of Protein Folds","authors":"D. Axe","doi":"10.5048/BIO-C.2010.1","DOIUrl":"https://doi.org/10.5048/BIO-C.2010.1","url":null,"abstract":"Four decades ago, several scientists suggested that the impossibility of any evolutionary process sampling anything but a miniscule fraction of the possible protein sequences posed a problem for the evolution of new proteins. This potential problem-the sampling problem -was largely ignored, in part because those who raised it had to rely on guesswork to fill some key gaps in their understanding of proteins. The huge advances since that time call for a careful reassessment of the issue they raised. Focusing specifically on the origin of new protein folds, I argue here that the sampling problem remains. The difficulty stems from the fact that new protein functions, when analyzed at the level of new beneficial phenotypes, typically require multiple new protein folds, which in turn require long stretches of new protein sequence. Two conceivable ways for this not to pose an insurmountable barrier to Darwinian searches exist. One is that protein function might generally be largely indifferent to protein sequence. The other is that relatively simple manipulations of existing genes, such as shuffling of genetic modules, might be able to produce the necessary new folds. I argue that these ideas now stand at odds both with known principles of protein structure and with direct experimental evidence. If this is correct, the sampling problem is here to stay, and we should be looking well outside the Darwinian framework for an adequate explanation of fold origins.","PeriodicalId":89660,"journal":{"name":"BIO-complexity","volume":"2010 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2010-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70593374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 19