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

存在两种方法来功能描述赋予每个生物体独特的遗传特征的遗传组成。第一种方法将特定的生物化学活动归因于基因组的特定部分，是描述性的和机械的;它没有回答因果关系和功能性的问题。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，以及它们在进化过程中是如何维持的。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）非功能性部分，这些部分通常对生物体的影响是惰性和无害的，但在某些情况下可能会对适应性产生不利影响。在这项研究期间，PI将直接让休斯顿大学的本科生和研究生以及休斯顿地区的其他机构通过WikiEdu和其他维基媒体渠道参与与进化生物学相关的写作活动。WikiEdu旨在将高等教育与维基百科连接起来，确保维基百科，世界上阅读量最大的信息来源，具有代表性，准确性和完整性。PI也是WikiJournal of Science的副编辑，该杂志发表评论文章。它实现了公众参与和推广，并通过出版的双重过程影响公众对科学的理解：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有了巨大的进步，但仍有必要系统地列举和讨论影响基因组的许多非适应性和反适应性进化过程和机制，并从逻辑上提出为什么“完美”不能成为任何自然过程的预期结果的原因。这些进化的非适应性和反适应性力量的综合，每一个都作为一个可检验的假设提出，并伴随着理论，实验和观察证据，将是一个受欢迎的适应性“只是这样的故事”的解毒剂。该合成具有另外的目的，即，说明“假设驱动的科学”优于所有其他调查方法，如“数据驱动的科学”，处理需要一个假设作为科学研究的中心概念化。这项研究将涉及许多原因，为什么进化的性质和它所采用的机制是无法产生任何接近完美的性能（即，获得的输出），效率（即，获得输出的方式）或适合性。从这种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。综合将包括理论以及经验的结果。一些导致进化“不完美”的进化因素将被考虑，例如，（1）缺乏反馈机制;（2）有效种群大小的限制;（3）突变的无差异性;（4）历史偶然性;（5）有害突变造成的遗传负荷;（6）灭绝的随机发生;（7）基因组性冲突，即两性基本上共享相同的基因组，但却受到不同的选择压力。该奖项反映了NSF的法定使命，并已被认为值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估来支持。

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.