The six articles of this section of the special issue explore philosophical questions of comparative biology, very broadly construed. Under this category, I place systematics, classification, and historical Darwinian evolutionary theory. Classic epistemic and metaphysical questions of comparative biology include: Are species natural kinds or individuals? What are the proper units of the biological hierarchy(ies) pertinent to evolution and classification? What is the fundamental relation between the Tree of Life and the Linnean Hierarchy? Why was Darwin’s (putative?) focus on variational rather than typological thinking so revolutionary? How does phylogenetic inference and reasoning work? Moreover, how should it work? How are parts of complex historical systems individuated? What would a historically sensitive notion of the biological function of structures, behaviors and characters look like? These questions have been investigated from a philosophical point of view at least since the seminal work of philosophers who started analytical philosophy of biology during the 1960s and 1970s, including David Hull, Michael Ruse, Elliot Sober, and William Wimsatt. Biologists such as Richard Lewontin, Ernst Mayr, and Stephen J. Gould have also contributed significantly to setting the question agenda on these matters. We find ourselves today at a dizzying time in biological research. Astounding data-driven progress is being made in a variety of broad biological fields including: (1) genomics, proteomics, and systems biology, (2) biodiversity and ecology, and (3) evolutionary developmental biology (‘‘evo-devo’’). This is not the place to substantiate the reality and depth of these research fields; I trust that that is clear and present to the reader. However, this is a place to argue that each of these growth fields relies heavily—if not explicitly, then certainly implicitly—on comparative biology. Briefly consider the following questions for each area: How do we investigate and discover the function of a particular gene or molecule? We perform a comparative analysis of that gene sequence or molecular structure across a range

中文翻译：

---

引言：从哲学的角度

本期特刊的六篇文章探讨了比较生物学的哲学问题，解释非常广泛。在这个类别下，我将系统学、分类和历史达尔文进化论放在一起。比较生物学的经典认知和形而上学问题包括：物种是自然种类还是个体？与进化和分类相关的生物等级的适当单位是什么？生命之树和林奈等级制度之间的基本关系是什么？为什么达尔文（假定的？）专注于变体而不是类型学思维如此具有革命性？系统发育推断和推理是如何工作的？而且，它应该如何工作？复杂历史系统的各个部分如何个体化？关于结构、行为和角色的生物学功能的历史敏感概念会是什么样子？至少自 1960 年代和 1970 年代开始生物学分析哲学的哲学家（包括大卫·赫尔、迈克尔·鲁斯、埃利奥特·索伯和威廉·威姆萨特）的开创性工作以来，人们一直从哲学的角度对这些问题进行了研究。Richard Lewontin、Ernst Mayr 和 Stephen J. Gould 等生物学家也为制定有关这些问题的问题议程做出了重大贡献。我们今天发现自己处于生物学研究的一个令人眼花缭乱的时期。在各种广泛的生物学领域正在取得惊人的数据驱动进展，包括：(1) 基因组学、蛋白质组学和系统生物学，(2) 生物多样性和生态学，以及 (3) 进化发育生物学 (''evo-devo'')。这不是证实这些研究领域的现实和深度的地方；我相信这很清楚并且呈现给读者。然而，这是一个争论这些增长领域中的每一个都严重依赖——如果不是明确的，那么肯定是隐含的——比较生物学的地方。简要考虑每个领域的以下问题： 我们如何研究和发现特定基因或分子的功能？我们对某个范围内的基因序列或分子结构进行比较分析 这是一个争论这些增长领域中的每一个都严重依赖——如果不是明确的，那么肯定是隐含的——比较生物学的地方。简要考虑每个领域的以下问题： 我们如何研究和发现特定基因或分子的功能？我们对某个范围内的基因序列或分子结构进行比较分析 这是一个争论这些增长领域中的每一个都严重依赖——如果不是明确的，那么肯定是隐含的——比较生物学的地方。简要考虑每个领域的以下问题： 我们如何研究和发现特定基因或分子的功能？我们对某个范围内的基因序列或分子结构进行比较分析