OPUS: CRS: Non-Adaptive and Anti-Adaptive Forces in Evolution, A Synthesis

存在两种方法来描述赋予每个生物体独特遗传特征的基因组成的功能。第一种方法，将特定的生化活动归因于基因组的特定部分，是描述性和机械性的；它没有回答因果关系和功能的问题。第二种方法是进化的；它着眼于基因组中的特定片段，并询问为什么这些片段存在，以及它们在进化时期是如何维持的。通过使用第二种方法，本研究将试图确定导致功能性和缺乏功能性的驱动力，从而使研究人员能够识别和关注(1)基因组的功能部分，以及(2)就其对生物体的影响而言通常是惰性和无害的非功能部分，但在某些情况下可能会对适应性产生不利影响。在这项研究中，PI将直接与休斯顿大学以及休斯顿地区其他机构的本科生和研究生进行交流，通过WikiEdu和其他维基媒体渠道进行与进化生物学相关的写作密集活动。WikiEdu旨在将高等教育与维基百科连接起来，确保维基百科这个世界上阅读量最大的信息源具有代表性、准确性和完整性。PI也是发表评论文章的维基科学杂志的副主编。它通过双重出版过程实现公众参与和推广，并影响公众对科学的理解：一篇标准的学术论文和维基百科上的可修改版本。尽管我们对进化过程的分子和随机基础的理解取得了巨大进步，但仍有必要系统地列举和讨论许多影响基因组的非适应性和反适应性进化过程和机制，并逻辑地提出“完美”不可能是任何自然过程预期结果的原因。将这些进化的非适应性和反适应性力量综合起来，每一种力量都可以作为一个可检验的假设，并伴随着理论、实验和观察证据，这将是一种受欢迎的解毒剂，可以消除适应性的“只是这样的故事”。这种综合还有一个额外的目的，即说明“假设驱动的科学”比所有其他探究方法（如“数据驱动的科学”）的优势，这些方法需要将假设作为科学研究的中心概念化。本研究将探讨为什么进化的本质及其所采用的机制无法在性能（即获得的输出）、效率（即获得输出的方式）或适应性方面产生任何接近完美的东西。从这一综合中得出的概念框架将用于分析和解释基因组水平上的进化模式和特征。综合将包括理论和实证结果。一些导致进化“不完善”的进化因素将被考虑，例如，(1)缺乏反馈机制；(2)有效种群规模的限制；(3)突变的无差异性；(4)历史偶然性；（五）有害突变造成的遗传负荷；（六）随机灭绝；(7)基因组性冲突，即两性共享本质上相同的基因组，但受制于不同的选择压力。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

There exist two approaches to the functional description of the genetic makeup that endows each living organism with its unique heritable characters. The first approach, which ascribes particular biochemical activities to particular parts of the genome, is descriptive and mechanistic; it does not answer questions of causality and functionality. The second approach is evolutionary; it looks at particular segments within the genome and asks why these segments exist and how are they maintained during evolutionary times. By using the second approach, this study will attempt to identify the driving forces that lead to functionality and lack of functionality, thereby enabling researchers to identify and focus on (1) the functional parts of the genome, and (2) on the nonfunctional parts that are usually inert and innocuous in terms of their effects on the organism, but which under certain circumstances may adversely affect fitness. During this study, the PI will directly engage undergraduate and graduate students at University of Houston as well as other institutions in the Houston area in writing-intense activities related to evolutionary biology through WikiEdu and other Wikimedia outlets. WikiEdu aims to connect higher education to Wikipedia, ensuring that Wikipedia, the world’s most read information source, is representative, accurate, and complete. The PI is also an associate editor of WikiJournal of Science, which publishes review articles. It achieves public engagement and outreach, and impacts public understanding of science by a dual process of publication: a standard academic paper and a modifiable version in Wikipedia. Despite huge advances in our understanding of the molecular and stochastic foundations of the evolutionary process, there is a need to systematically enumerate and discuss the many non-adaptive and anti-adaptive evolutionary processes and mechanisms affecting the genome and to logically present the reasons why “perfection” cannot be the expected outcome of any natural process. A synthesis of these evolutionary non-adaptive and anti-adaptive forces, each presented as a testable hypothesis and accompanied by theoretical, experimental, and observational evidence would be a welcome antidote to adaptive “just-so stories.” This synthesis has an additional aim, i.e., to illustrate the advantages of “hypothesis-driven science” over all other methods of inquiry, such as “data-driven science,” that dispose with the need for a hypothesis as the central conceptualization of scientific research. This research will deal with the many reasons why evolution by its nature and the mechanisms it employs is incapable of producing anything approaching perfection in terms of performance (i.e., the attained output), efficiency (i.e., the manner with which the output is attained), or fitness. The conceptual framework derived from this synthesis will be used to analyze and interpret evolutionary patterns and characteristics at the genome level. The synthesis will encompass theoretical as well as empirical results. A number of evolutionary factors leading to evolutionary “imperfections” will be considered, for example, (1) the lack of feedback mechanisms; (2) the limitations imposed by the effective population size; (3) the indifference of mutations, (4) historical contingency; (5) the genetic load imposed by deleterious mutations, (6) random occurrences of extinction; and (7) genomic sexual conflicts, whereby the two sexes share essentially the same genomes yet are subject to divergent selection pressures.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.