Water availability has a decisive impact on plant growth, survival and distribution. Climate change is expected to alter both the amount and variability of precipitation. To predict and understand plant responses to water stress, efficient and robust mechanisms for describing their functional responses to water availability are needed. However, most ecohydrological processes and models which take into account these responses are inherently complex, difficult to understand and require large amounts of data. We develop a novel straightforward approach and hypothesize that: (1) Plants exhibit two archetypical response patterns under water stress, one typical to slow-growing plants and one typical to fast-growing ones, with most plants being situated between these two. (2) Differences within and between these functional types can be adequately described by a single parameter - the threshold of relative soil water content - at which plants reduce their transpiration in response to water stress. This indicator is straightforward and relies on data which is relatively easy to measure. Its effect has been previously described and it is already used in several models to simulate the effect of water stress on plants. In our approach, we combine this indicator with a description of reactions patterns. This combination provides a general and efficient way of classifying plant responses and allows the assessment of the impact of water stress on a wide variety of plants. Due to its simplicity, our approach offers the opportunity to include water relations of plants in a larger set of models and descriptions than it is possible with more complex ecohydrological descriptions. It also can be used to explain biodiversity in fluctuating environments.
{"title":"Conservatives and Gamblers: Interpreting plant functional response to water stress in terms of a single indicator","authors":"Martin Kazmierczak, K. Johst, A. Huth","doi":"10.4033/IEE.2015.8.5.N","DOIUrl":"https://doi.org/10.4033/IEE.2015.8.5.N","url":null,"abstract":"Water availability has a decisive impact on plant growth, survival and distribution. Climate change is expected to alter both the amount and variability of precipitation. To predict and understand plant responses to water stress, efficient and robust mechanisms for describing their functional responses to water availability are needed. However, most ecohydrological processes and models which take into account these responses are inherently complex, difficult to understand and require large amounts of data. We develop a novel straightforward approach and hypothesize that: (1) Plants exhibit two archetypical response patterns under water stress, one typical to slow-growing plants and one typical to fast-growing ones, with most plants being situated between these two. (2) Differences within and between these functional types can be adequately described by a single parameter - the threshold of relative soil water content - at which plants reduce their transpiration in response to water stress. This indicator is straightforward and relies on data which is relatively easy to measure. Its effect has been previously described and it is already used in several models to simulate the effect of water stress on plants. In our approach, we combine this indicator with a description of reactions patterns. This combination provides a general and efficient way of classifying plant responses and allows the assessment of the impact of water stress on a wide variety of plants. Due to its simplicity, our approach offers the opportunity to include water relations of plants in a larger set of models and descriptions than it is possible with more complex ecohydrological descriptions. It also can be used to explain biodiversity in fluctuating environments.","PeriodicalId":42755,"journal":{"name":"Ideas in Ecology and Evolution","volume":"8 1","pages":""},"PeriodicalIF":0.2,"publicationDate":"2015-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70235852","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}
There exists discordance between different levels of evolution because the whole often differs from the sum of the parts. Yet, it is not obvious that the new term 'stoch-aptation' clarifies these differences between evolutionary levels, especially when this term seems largely equivalent to stochastic drift, to mega-evolution, and maybe even to phenotypic plasticity with extreme environments. But this new term forces us to carefully examine what evolutionary biologists mean by randomness, drift, selection, plasticity, and mega-evolution.
{"title":"Wherefore stoch-aptation?","authors":"Root Gorelick","doi":"10.4033/IEE.2015.8.7.C","DOIUrl":"https://doi.org/10.4033/IEE.2015.8.7.C","url":null,"abstract":"There exists discordance between different levels of evolution because the whole often differs from the sum of the parts. Yet, it is not obvious that the new term 'stoch-aptation' clarifies these differences between evolutionary levels, especially when this term seems largely equivalent to stochastic drift, to mega-evolution, and maybe even to phenotypic plasticity with extreme environments. But this new term forces us to carefully examine what evolutionary biologists mean by randomness, drift, selection, plasticity, and mega-evolution.","PeriodicalId":42755,"journal":{"name":"Ideas in Ecology and Evolution","volume":"8 1","pages":""},"PeriodicalIF":0.2,"publicationDate":"2015-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70235990","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}
Following two seminal papers published in the journal Paleobiology by Stephen Jay Gould and Elisabeth Vrba several decades ago, I suggest a new term (stoch-aptation) to refer to those individual traits or sets of traits that provide, just by chance, fitness adventages to species when faced with catastrophes (i.e. geological events triggering massive mortality), and that may lead to the origin of taxonomical entities above the species level. I provide as an example of stoch-aptations the set of features that helped mammals pass the Cretaceous-Paleogene transition, as well as traits behind the success of living fossils. However, the identification of specific stoch-aptations can be difficult. This missing term is necessary and useful to (a) consolidate the idea of selection at different hierarchical levels, (b) acknowledge the role of chance in the evolution of higher taxonomical categories and (c) think of the role of geological catastrophes as generators of innovation.
继Stephen Jay Gould和Elisabeth Vrba几十年前在《古生物学》杂志上发表的两篇开创性论文之后，我提出了一个新术语(随机适应)，指的是那些个体特征或特征集，它们在面对灾难(即引发大规模死亡的地质事件)时偶然地为物种提供适应性优势，并可能导致物种水平以上的分类实体的起源。我提供了一组帮助哺乳动物通过白垩纪-古近纪过渡的特征，以及活化石成功背后的特征，作为一个例子。然而，确定具体的股票偏好可能是困难的。这个缺失的术语对于以下方面是必要和有用的:(a)巩固不同层次的选择观念，(b)承认机会在高级分类类别的进化中所起的作用，以及(c)考虑地质灾难作为创新的发电机的作用。
{"title":"Stoch-aptation: a new term in evolutionary biology and paleontology","authors":"A. Martínez‐Abraín","doi":"10.4033/IEE.2015.8.6.N","DOIUrl":"https://doi.org/10.4033/IEE.2015.8.6.N","url":null,"abstract":"Following two seminal papers published in the journal Paleobiology by Stephen Jay Gould and Elisabeth Vrba several decades ago, I suggest a new term (stoch-aptation) to refer to those individual traits or sets of traits that provide, just by chance, fitness adventages to species when faced with catastrophes (i.e. geological events triggering massive mortality), and that may lead to the origin of taxonomical entities above the species level. I provide as an example of stoch-aptations the set of features that helped mammals pass the Cretaceous-Paleogene transition, as well as traits behind the success of living fossils. However, the identification of specific stoch-aptations can be difficult. This missing term is necessary and useful to (a) consolidate the idea of selection at different hierarchical levels, (b) acknowledge the role of chance in the evolution of higher taxonomical categories and (c) think of the role of geological catastrophes as generators of innovation.","PeriodicalId":42755,"journal":{"name":"Ideas in Ecology and Evolution","volume":"8 1","pages":""},"PeriodicalIF":0.2,"publicationDate":"2015-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4033/IEE.2015.8.6.N","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70235862","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}
{"title":"Graduate student mentoring of undergraduates in the context of multi-level mentoring: Individual, departmental, and university responsibilities","authors":"B. Stoffer","doi":"10.4033/IEE.2015.8.4.C","DOIUrl":"https://doi.org/10.4033/IEE.2015.8.4.C","url":null,"abstract":"","PeriodicalId":42755,"journal":{"name":"Ideas in Ecology and Evolution","volume":"8 1","pages":""},"PeriodicalIF":0.2,"publicationDate":"2015-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4033/IEE.2015.8.4.C","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70235840","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}
In an earlier work, we found that 66% of manuscripts that suffered editorial rejections were finally accepted in journals of similar ranking to which they were originally submitted. We thus concluded that editors appear to be “poor oracles” with regards to being able evaluate the quality of a manuscript without the help of external reviewers. This article was recently criticized by the team of editors of the Ecological Society of America . In this work, we clarify some misunderstandings and offer new evidence supporting our view that external reviews should be the rule in the process of publishing scientific literature. Specifically, here we argue that (a) the claim that editorial rejections are based on manuscripts not adjusting to the journal’s scope rather than on academic quality is unconvincing; (b) if academic quality is being assessed to decide the fate of a submitted paper, this attribute must be evaluated including several external opinions and not only the superficial reading of one person, (c) our survey design was appropriate and, despite the small sample size, the conclusion that editors are poor oracles seems to be fairly reliable and, (d) the practice of sending the majority of submitted papers to external review should not cause the collapse of most popular journals. We insist that for the sake of science, editors need the opinion of external experts and should not act as oracles
{"title":"Are editors of ecological journals good oracles? A reply to Schimel et al. (2014) about the malpractice of editorial rejections","authors":"A. Farji-Brener, T. Kitzberger","doi":"10.4033/IEE.2015.8.1.F","DOIUrl":"https://doi.org/10.4033/IEE.2015.8.1.F","url":null,"abstract":"In an earlier work, we found that 66% of manuscripts that suffered editorial rejections were finally accepted in journals of similar ranking to which they were originally submitted. We thus concluded that editors appear to be “poor oracles” with regards to being able evaluate the quality of a manuscript without the help of external reviewers. This article was recently criticized by the team of editors of the Ecological Society of America . In this work, we clarify some misunderstandings and offer new evidence supporting our view that external reviews should be the rule in the process of publishing scientific literature. Specifically, here we argue that (a) the claim that editorial rejections are based on manuscripts not adjusting to the journal’s scope rather than on academic quality is unconvincing; (b) if academic quality is being assessed to decide the fate of a submitted paper, this attribute must be evaluated including several external opinions and not only the superficial reading of one person, (c) our survey design was appropriate and, despite the small sample size, the conclusion that editors are poor oracles seems to be fairly reliable and, (d) the practice of sending the majority of submitted papers to external review should not cause the collapse of most popular journals. We insist that for the sake of science, editors need the opinion of external experts and should not act as oracles","PeriodicalId":42755,"journal":{"name":"Ideas in Ecology and Evolution","volume":"8 1","pages":""},"PeriodicalIF":0.2,"publicationDate":"2015-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70235133","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}
The perception component of the language faculty and the teleological notion that everything may have intentions and purpose could have developed from the primitive agency detection seen in most moving animals. Many new-born, totally naive animals show predator avoidance and behave as if everything around may be alive and dangerous and have malevolent intentions. Piaget demonstrated that young children believe that everything around is probably alive and has purpose and intentions. The perception component of the language faculty involves an intrinsic motivation to search for intentions and meanings of sound combinations (words and phrases), and a search for the meanings and intentions of systematic changes in words, that is a search for the grammar rules. Possible homologs to animal genes for predator avoidance or perception of calls could be compared in humans and chimpanzees. Evidence of positive selection or accelerated evolution of human homolog genes might indicate putative genes for language perception.
{"title":"Possible evolution of teleological bias, language acquisition, and search for meaning from primitive agency detection","authors":"K. Engvild","doi":"10.4033/IEE.2015.8.2.N","DOIUrl":"https://doi.org/10.4033/IEE.2015.8.2.N","url":null,"abstract":"The perception component of the language faculty and the teleological notion that everything may have intentions and purpose could have developed from the primitive agency detection seen in most moving animals. Many new-born, totally naive animals show predator avoidance and behave as if everything around may be alive and dangerous and have malevolent intentions. Piaget demonstrated that young children believe that everything around is probably alive and has purpose and intentions. The perception component of the language faculty involves an intrinsic motivation to search for intentions and meanings of sound combinations (words and phrases), and a search for the meanings and intentions of systematic changes in words, that is a search for the grammar rules. Possible homologs to animal genes for predator avoidance or perception of calls could be compared in humans and chimpanzees. Evidence of positive selection or accelerated evolution of human homolog genes might indicate putative genes for language perception.","PeriodicalId":42755,"journal":{"name":"Ideas in Ecology and Evolution","volume":"8 1","pages":""},"PeriodicalIF":0.2,"publicationDate":"2015-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4033/IEE.2015.8.2.N","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70235348","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}
This article serves as a short 'best practices' aimed at graduate students for advising undergraduates, specifically within the disciplines of ecology and evolution. It offers documented research on undergraduate research experiences, and the most effective mentoring strategies for success across Science, Technology, Engineering, and Mathematics (STEM) disciplines, as well as practical methods for how to enact these strategies. Most importantly, this work serves particularly to highlight issues undergraduates may encounter in conducting research specifically in ecology and evolution, and what graduate student mentors can do to help students overcome these challenges.
{"title":"Modern graduate student mentors: Evidence-based best practices and special considerations for mentoring undergraduates in ecology and evolution","authors":"E. Weigel","doi":"10.4033/IEE.2015.8.3.C","DOIUrl":"https://doi.org/10.4033/IEE.2015.8.3.C","url":null,"abstract":"This article serves as a short 'best practices' aimed at graduate students for advising undergraduates, specifically within the disciplines of ecology and evolution. It offers documented research on undergraduate research experiences, and the most effective mentoring strategies for success across Science, Technology, Engineering, and Mathematics (STEM) disciplines, as well as practical methods for how to enact these strategies. Most importantly, this work serves particularly to highlight issues undergraduates may encounter in conducting research specifically in ecology and evolution, and what graduate student mentors can do to help students overcome these challenges.","PeriodicalId":42755,"journal":{"name":"Ideas in Ecology and Evolution","volume":"8 1","pages":""},"PeriodicalIF":0.2,"publicationDate":"2015-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70235778","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}
Gynogenetic organisms are asexual females of one species that require sperm from males of another species to initiate reproduction (but except in rare instances of ‘paternal leakage’, those sperm do not contribute to the genetic make-up of the gynogens’ offspring). Gynogenetic organisms seem to combine disadvantages of both sexual and asexual reproductive strategies (e.g., mating costs, reduced genetic diversity). We borrowed logic from the Red Queen Hypothesis (RQH) to help explain the persistence of gynogenetic species in nature, which is a paradox. The RQH is the most oft-cited explanation for the maintenance of sex. It states that evolving enemies generate a constantly changing environment, which provides the conditions that make sex advantageous. Under this scenario, asexual organisms cannot evolve fast enough to ‘keep up’ with co-evolving parasites and disease causing organisms, and ultimately show reduced fitness compared to sexual individuals. The RQH tends to view asexuality generally, ignoring important nuance in nature like gynogenetic species in mixed assemblages with closely related sexual species. We outline tests of the argument that sperm dependency prevents asexual gynogens from outcompeting sexuals in mixed species assemblages and that this further allows gynogens to escape evolving enemies.
{"title":"Do gynogenetic species escape evolving enemies","authors":"F. Dargent, M. Forbes","doi":"10.4033/IEE.2015.8.14.N","DOIUrl":"https://doi.org/10.4033/IEE.2015.8.14.N","url":null,"abstract":"Gynogenetic organisms are asexual females of one species that require sperm from males of another species to initiate reproduction (but except in rare instances of ‘paternal leakage’, those sperm do not contribute to the genetic make-up of the gynogens’ offspring). Gynogenetic organisms seem to combine disadvantages of both sexual and asexual reproductive strategies (e.g., mating costs, reduced genetic diversity). We borrowed logic from the Red Queen Hypothesis (RQH) to help explain the persistence of gynogenetic species in nature, which is a paradox. The RQH is the most oft-cited explanation for the maintenance of sex. It states that evolving enemies generate a constantly changing environment, which provides the conditions that make sex advantageous. Under this scenario, asexual organisms cannot evolve fast enough to ‘keep up’ with co-evolving parasites and disease causing organisms, and ultimately show reduced fitness compared to sexual individuals. The RQH tends to view asexuality generally, ignoring important nuance in nature like gynogenetic species in mixed assemblages with closely related sexual species. We outline tests of the argument that sperm dependency prevents asexual gynogens from outcompeting sexuals in mixed species assemblages and that this further allows gynogens to escape evolving enemies.","PeriodicalId":42755,"journal":{"name":"Ideas in Ecology and Evolution","volume":"8 1","pages":""},"PeriodicalIF":0.2,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70235560","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}
The progress of science requires inspiration. Some researchers find this only from data. "Show me the evidence", they say. Many peer-reviewed publications in science, however, have no data. They involve a different kind of inspiration: proposals for original ideas or new hypothesis development. These are found within the 'Forum', 'Perspectives', 'Opinion' and 'Commentary' sections of many journals, and in some journals, like IEE, devoted entirely to new ideas and commentary. I have always been particularly drawn to the honesty and beauty in this creative brand of enquiry. And so I am puzzled to hear it often dismissed out of hand with pejorative labeling, like ‘hand-waving’ and ‘just-sostories’. Many—especially among the elites and selfappointed guardians of established theory—would have us believe that only ‘evidence-based’ practice and products can be taken seriously as legitimate sources of inspiration and discovery. This is plainly arrogant and wrongheaded. The scientific method means doing whatever is necessary to get good answers to questions worth asking. And so data collection that is not guided by interesting, novel, and important ideas is usually boring at best. At worst, it is a waste of research grant funds. But published data are plagued with an even more serious problem: we never know how much to trust them. A few minutes of Google searching under the terms "research bias", "scientific misconduct", "publication bias", and “retractions” shows that the follies of faith in published data have come sharply and painfully into the public spotlight in recent years. The latest bad news is particularly troubling: most published studies are not reproducible (Baker 2015, Bartlett 2015, Begley et al 2015, Jump 2015). The statistical implication from this is unavoidable: it means that the results of at least half of all empirical research that has ever been published, probably in all fields of study, are inconclusive at best. They may be reliable and useful, but maybe not. Mounting evidence in fact leans toward the latter (Ioannidis 2005, Lehrer 2010,Hayden 2013). Moreover, these inconclusive reports, I suspect, are likely to involve mostly those that had been regarded as especially promising contributions—lauded as particularly novel and ground-breaking. In contrast, the smaller group that passed the reproducibility test is likely to involve mostly esoteric research that few people care about, or so-called ‘safe research’: studies that report merely confirmatory results, designed to generate data that were already categorically expected, i.e. studies that aimed to provide just another example of support for well-established theory—or if not the latter, support for something that was already an obvious bet or easily believable anyway, even without data collection (or theory). A study that anticipates only positive results in advance is pointless. There is no reason for doing the science in the first place; it just confirms what one already knows
科学的进步需要灵感。一些研究人员仅从数据中发现了这一点。“出示证据”，他们说。然而，许多同行评议的科学出版物没有数据。它们涉及一种不同的灵感:对原始想法或新假设发展的建议。在许多期刊的“论坛”、“观点”、“观点”和“评论”部分，以及在一些期刊(如IEE)中，它们完全致力于新思想和评论。我一直特别被这种创造性探索中的诚实和美丽所吸引。因此，我很困惑地听到它经常被立即贴上贬义的标签，比如“挥手”和“只是一些故事”。许多人——尤其是精英和自封的既有理论的捍卫者——会让我们相信，只有“基于证据的”实践和产品才能被认真地视为灵感和发现的合法来源。这显然是傲慢和错误的。科学的方法意味着做任何必要的事情来得到值得问的问题的好答案。因此，没有有趣、新颖和重要想法的数据收集通常最多是无聊的。最坏的情况是，这是对研究经费的浪费。但已公布的数据还存在一个更严重的问题:我们永远不知道该在多大程度上信任它们。在谷歌上搜索几分钟“研究偏见”、“科学不端行为”、“发表偏见”和“撤回”就会发现，近年来，对已发表数据的愚蠢信仰已经尖锐而痛苦地成为公众关注的焦点。最新的坏消息尤其令人不安:大多数发表的研究都是不可重复的(Baker 2015, Bartlett 2015, Begley et al 2015, Jump 2015)。由此产生的统计含义是不可避免的:这意味着，至少有一半已发表的实证研究(可能涉及所有研究领域)的结果充其量是不确定的。它们可能是可靠和有用的，但也可能不是。事实上，越来越多的证据倾向于后者(Ioannidis 2005, Lehrer 2010,Hayden 2013)。此外，我怀疑，这些不确定的报告可能主要涉及那些被视为特别有前途的贡献——被称赞为特别新颖和突破性的。相比之下，通过可重复性测试的小群体可能主要涉及很少有人关心的深奥研究，或所谓的“安全研究”:仅报告证实性结果的研究，旨在产生已经明确预期的数据，即旨在为已确立的理论提供支持的另一个例子的研究——或者，如果不是后者，支持已经是一个明显的打赌或很容易相信的东西，即使没有数据收集(或理论)。一项事先只预测积极结果的研究是毫无意义的。一开始就没有理由做科学研究;它只是证实了一个人已经知道的一定是真的。这可能解释了为什么大多数已发表的研究在文献中仍然没有被引用-或者实际上是这样，只吸引了少数引用，其中许多(或大多数)是自我引用(Bauerlein et al. 2010)。对于这种再现性问题有什么补救办法吗?毫无疑问，有一些是不可复制的，研究人员正在争分夺秒地努力识别它们[参见Nature Special (2015) on Challenges in reproducibility Research, http://www.nature.com/news/reproducibility1.17552]。有效地解决这些问题(如果有可能的话)将需要完全重构科学文化，使用新的和修订的“最佳实践”手册(例如见Nosek等人)。
{"title":"The problem with data","authors":"L. Aarssen","doi":"10.4033/IEE.2015.8.15.E","DOIUrl":"https://doi.org/10.4033/IEE.2015.8.15.E","url":null,"abstract":"The progress of science requires inspiration. Some researchers find this only from data. \"Show me the evidence\", they say. Many peer-reviewed publications in science, however, have no data. They involve a different kind of inspiration: proposals for original ideas or new hypothesis development. These are found within the 'Forum', 'Perspectives', 'Opinion' and 'Commentary' sections of many journals, and in some journals, like IEE, devoted entirely to new ideas and commentary. I have always been particularly drawn to the honesty and beauty in this creative brand of enquiry. And so I am puzzled to hear it often dismissed out of hand with pejorative labeling, like ‘hand-waving’ and ‘just-sostories’. Many—especially among the elites and selfappointed guardians of established theory—would have us believe that only ‘evidence-based’ practice and products can be taken seriously as legitimate sources of inspiration and discovery. This is plainly arrogant and wrongheaded. The scientific method means doing whatever is necessary to get good answers to questions worth asking. And so data collection that is not guided by interesting, novel, and important ideas is usually boring at best. At worst, it is a waste of research grant funds. But published data are plagued with an even more serious problem: we never know how much to trust them. A few minutes of Google searching under the terms \"research bias\", \"scientific misconduct\", \"publication bias\", and “retractions” shows that the follies of faith in published data have come sharply and painfully into the public spotlight in recent years. The latest bad news is particularly troubling: most published studies are not reproducible (Baker 2015, Bartlett 2015, Begley et al 2015, Jump 2015). The statistical implication from this is unavoidable: it means that the results of at least half of all empirical research that has ever been published, probably in all fields of study, are inconclusive at best. They may be reliable and useful, but maybe not. Mounting evidence in fact leans toward the latter (Ioannidis 2005, Lehrer 2010,Hayden 2013). Moreover, these inconclusive reports, I suspect, are likely to involve mostly those that had been regarded as especially promising contributions—lauded as particularly novel and ground-breaking. In contrast, the smaller group that passed the reproducibility test is likely to involve mostly esoteric research that few people care about, or so-called ‘safe research’: studies that report merely confirmatory results, designed to generate data that were already categorically expected, i.e. studies that aimed to provide just another example of support for well-established theory—or if not the latter, support for something that was already an obvious bet or easily believable anyway, even without data collection (or theory). A study that anticipates only positive results in advance is pointless. There is no reason for doing the science in the first place; it just confirms what one already knows","PeriodicalId":42755,"journal":{"name":"Ideas in Ecology and Evolution","volume":"8 1","pages":""},"PeriodicalIF":0.2,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70235144","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}
Should asexual/vegetative offspring be counted in estimates of evolutionary fitness in seed plants? The answer it seems remains debatable among evolutionary ecologists. Arguably, however, the answer is yes when fitness is ascribed strictly to resident genes/alleles, in terms of their survival—through copying and transmission success—over time. This success results only because sporophyte ‘rooted units’ make more ‘rooted units’—not primarily in terms of leaving descendent ‘individuals’, but more fundamentally as carriers of gene/allele copies in perpetuity. The ‘rooted-unit’ (RU) is identified by root and shoot tissue integrated through an essential, and distinctly local, vascular transition. It thus represents a functional and practical circumscription for enumerating individual ‘offspring’ that applies equally to those derived from zygotes, or from clonality. This ‘binary’ nature of fitness estimation in seed plants remains legitimate despite that clonal RU offspring are normally all genotypically identical; the same is true of zygotic/seed-derived RU offspring produced by apomixis or from inbred sexual lines (and somatic mutation sometimes means that clonal offspring are not, in fact, genotypically identical). Neither is this fitness estimation compromised if a young clonal RU offspring, during establishment, temporarily receives resource translocation from connection to a parental RU; the same is true for immature zygotic offspring that receive maternal resources within the seed, via female gametophyte or endosperm/ perisperm tissue. Finally, the above fitness estimate also remains uncompromised even if there is facilitation between mature neighbouring RUs that remain connected with lifetime physiological integration; analogous facilitation also occurs routinely between neighbouring RUs in aclonal species.
{"title":"Estimating fitness from offspring counts in clonal seed plants","authors":"L. Aarssen","doi":"10.4033/IEE.2014.7.16.C","DOIUrl":"https://doi.org/10.4033/IEE.2014.7.16.C","url":null,"abstract":"Should asexual/vegetative offspring be counted in estimates of evolutionary fitness in seed plants? The answer it seems remains debatable among evolutionary ecologists. Arguably, however, the answer is yes when fitness is ascribed strictly to resident genes/alleles, in terms of their survival—through copying and transmission success—over time. This success results only because sporophyte ‘rooted units’ make more ‘rooted units’—not primarily in terms of leaving descendent ‘individuals’, but more fundamentally as carriers of gene/allele copies in perpetuity. The ‘rooted-unit’ (RU) is identified by root and shoot tissue integrated through an essential, and distinctly local, vascular transition. It thus represents a functional and practical circumscription for enumerating individual ‘offspring’ that applies equally to those derived from zygotes, or from clonality. This ‘binary’ nature of fitness estimation in seed plants remains legitimate despite that clonal RU offspring are normally all genotypically identical; the same is true of zygotic/seed-derived RU offspring produced by apomixis or from inbred sexual lines (and somatic mutation sometimes means that clonal offspring are not, in fact, genotypically identical). Neither is this fitness estimation compromised if a young clonal RU offspring, during establishment, temporarily receives resource translocation from connection to a parental RU; the same is true for immature zygotic offspring that receive maternal resources within the seed, via female gametophyte or endosperm/ perisperm tissue. Finally, the above fitness estimate also remains uncompromised even if there is facilitation between mature neighbouring RUs that remain connected with lifetime physiological integration; analogous facilitation also occurs routinely between neighbouring RUs in aclonal species.","PeriodicalId":42755,"journal":{"name":"Ideas in Ecology and Evolution","volume":"7 1","pages":""},"PeriodicalIF":0.2,"publicationDate":"2014-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70234626","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}
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