题目：走向“后基因组时代”的遗传科学与生命进化问题辨析
作者：李曈
指导老师：刘大椿
答辩时间：2018年5月14日
目 录
绪 论
0.1 论文研究背景
0.1.1 当代遗传科学的发展与新的问题
0.1.2 当代进化论的发展与新的问题
0.1.3 遗传科学与进化论的相互渗透
0.2 文献综述
0.3 选题意义与论文框架
0.3.1 选题意义
0.3.2 论文框架
第1章走向后基因组时代的遗传科学
1.1 遗传科学的三个发展阶段
1.1.1 1900-1953：经典遗传学时代
1.1.2 1953-2000：分子遗传学时代
1.1.3 2000至今：后基因组时代
1.2 基因研究的功能转向
1.2.1 功能基因组学取代结构基因组学
1.2.2 解释基因功能的两种视角
1.3 基因中心主义的消解
1.3.1 表观遗传现象对经典定律及中心法则的反叛
1.3.2 渠化现象对表型在进化中作用的强调
1.3.3 围绕拉马克主义产生新的争论
本章小结
第2章进化理论的演变
2.1 从进化思想到群体遗传学
2.1.1 达尔文之前的进化思想
2.1.2 达尔文的进化论
2.1.3 达尔文主义与基因学说的“现代综合”
2.1.4 进化中基因作用的中性假说修正
2.1.5 遗传科学与进化论的错位
2.2 基于自然选择的三种进化模型
2.2.1 进步主义的阶梯模型
2.2.2 人类中心主义的倒锥模型
2.2.3 进化历史主义的支流模型
2.3 复杂性科学对进化图景的修正
2.3.1 广义进化综合理论
2.3.2 自创生-盖娅理论的进化图景
2.3.3 对新达尔文主义的批判与补充
本章小结
第3章遗传与进化问题中的基因还原论辨析
3.1 遗传科学中的基因还原论
3.1.1 关于基因的弱微观还原论
3.1.2 关于基因的强微观还原论
3.1.3 作为基因决定论的还原论
3.1.4 基因还原论的应用：优生学
3.2 进化论中的基因还原论
3.2.1 进化论中基因还原论的背景
3.2.2 自私基因论的假设与问题
3.2.3 基因还原论的衍生：模因论
本章小结
第4章遗传与进化视角的人性论解释
4.1 社会生物学对人性的解释
4.1.1 社会生物学的创立
4.1.2 社会生物学的基因还原论倾向
4.1.3 对社会生物学的自然主义之批判
4.2 演化心理学对人性的解释
4.2.1 演化心理学的基本假设
4.2.2 演化心理学存在的问题
4.3 基于基因选择论的人性解释
4.3.1 道金斯在人性论上的思想变化
4.3.2 对该人性论的两种发展
4.3.3 两种人性假设的对比
4.4 遗传与进化解释视角的局限
4.4.1 泛生物学解释的限度
4.4.2 二元论批判的不彻底性
本章小结
结语：走出基因中心主义
5.1 研究总结
5.1.1 后基因组时代是当下遗传科学的研究共识
5.1.2 遗传科学呈现功能转向和去中心化特征
5.1.3 遗传科学与进化论对基因的定义出现错位
5.1.4 遗传学新证据对基因还原论的合理性构成挑战
5.1.5 生物学视角对人性论的解释存在局限
5.2 展望：从基因中心主义转向情境主义
5.2.1 基因研究的去中心化
5.2.2 发育学对遗传学的补充
参考文献
致 谢
摘 要
“基因”是20世纪科学界的关键词。以1900年孟德尔遗传学的重新发现为开端，到2000年人类基因组计划（Human Genome Project）取得初步成果，仅有百年历史的遗传科学重塑了人类对生命的理解。然而进入21世纪，越来越多无法被经典遗传学解释的反例涌现出来。另一个新的名词——“后基因组时代”（the Post-genomic Era）成为学界争论的焦点。核心问题在于：20世纪的遗传科学很可能从本质上误解了“基因”的含义。若是如此，以基因学说为基础的遗传科学、进化理论，甚至相关的社会理论，都将要面临一场大的变革。是故，本文从遗传科学的最新争论为切入点，试探讨围绕“后基因组时代”的一系列理论转变，以及遗传科学与进化论在新时代将面临的挑战。
本文第一章梳理了遗传科学的百年历史和21世纪的前沿动态。通常来论，遗传科学以孟德尔遗传学重新发现、DNA双螺旋结构揭晓、人类基因组草图完成为标志，分别划为经典遗传学时代、分子遗传学时代、后基因组时代三个阶段。每个阶段中，作为核心术语的“基因”都有着不同的定义。特别是在后基因组时代，为了应对不断出现的新科学证据，众多科学家都对基因进行了重新定义。这些定义存在诸多分歧，但都表现出功能转向与去中心化的特点。与此同时，调控因子、表观遗传等非基因遗传现象引起了广泛关注，甚至引发了“新拉马克主义”的争论。可以预见的是，后基因组时代的遗传科学将颠覆先前人们对生命机制的理解，其影响也将不断扩散到各个相关领域。
本文第二章关注了与遗传科学最直接相关的进化论领域。虽然在最初，由于孟德尔的研究被埋没，尚无人将其与达尔文进化论相联系。但在1900年孟德尔遗传学再度发现之后，致力于统计学应用的生物学家们迅速发现了二者之间的密切联系。以遗传科学为基础的“新达尔文主义”得以建立，遗传与进化两大主题的联姻成就了生物学的“现代综合”（modern synthesize）。基因学说成为进化论的微观基础。然而在20世纪末，从复杂性科学领域兴起的系统自然观冲击了新达尔文主义的经典理论，异军突起的“自创生-盖娅”（self creation - Gaia）假说与后基因组时代新遗传学证据一起，成为进化论在21世纪必须面对的问题。
本文第三章关注了遗传与进化领域的基因还原论问题。与一般还原论不同，基因还原论不是通常讨论的实体还原或结构还原，而是一种构成信息的还原。在遗传科学中，由于社会达尔文主义的余波，基因还原论的讨论与应用存在大量误解。但随着后基因组时代的功能转向与去中心化，以还原论为基础的优生学势必将转向由发育学所主导的情境主义优境学（euthenics）。在进化论中，基因还原论主要表现为理查德·道金斯（Richard Dawkins）为代表的“自私基因论”（the Selfish Gene），即一种选择层次的基因还原论。然而道金斯所定义的“基因”并不能与后基因组时代的新遗传学相兼容，其所衍生的“模因”（meme）假说更是存在问题的。
本文第四章延伸到以遗传和进化理论为基础的人性论探讨。虽然社会达尔文主义逐渐被学界抛弃，其所引发的“寻找人性的自然基础”问题却从未停息。从20世纪末至今，几个具有代表性的理论一度成为了生物学与社会学讨论的热点，主要包括社会生物学（sociobiology）、演化心理学（evolutionary psychology）、达尔文左派（Darwinian Left）等思想。这些理论大部分是由生物学家所提出，并将具有遗传和进化特性的基因作为人性的自然基础，试图消解以往人性论中“先天遗传（自然）与后天培育（社会）”的经典二元论。然而，由于泛生物学解释的局限，这些理论对二元论的批判并不彻底。至后基因组时代，对基因的重新定义将会为重释人性的自然基础提供新的出路。
最后，本文总结了在后基因组时代的开端，遗传与进化研究所达成的几个关键结论，并提出由基因中心论向情境主义转变的趋势展望。由于基因表达取代基因结构成为遗传科学的研究重点，发育学不仅推动了优生学向优境学转向，更是基因与非基因遗传研究不可或缺的视角。同时，新兴的演化发育生物学（evolutionary developmental biology）也将发育学与进化论研究结合起来。不同于20世纪的经典遗传科学与进化论研究，发育学强调基因在具体情境中的表达，包括基因的微环境、生物体内环境，乃至自然界与人类社会的外在环境。情境主义或将成为后基因组时代的主题，并为弥合自然与社会的二分、解释生命本质问题提供新的路径。
关键词：基因; 遗传; 进化; 后基因组时代
ABSTRACT
"Gene" is a key word of science in the 20th century. From 1900 when Mendel's genetic theory was rediscoveried, to Human Genome Project gained its first achievement in 2000, genetics which has only one hundred years' history, had totally redefined human's understanding of life. However, with the development of genome studies in the 21th century, more and more counter-examples appeared which cannot be explained by the classic theories. Instead, a new key word -- "the Post-genomic Era" became the bone of contention. And the core problem is that the 20 century genetics very probably misunderstood the essense of "gene". If so, theories based on gene such as genetics, evolution, and even certain social theories, will face a big revolution. For that reason, this dissertation will start at the latest dispute in genetics, and then discuss what challenges genetics and evolution studies are facing in this new era.
The first chapter is about the 100 years' history and the leading edge of genetics. Generally, the development of genetics can be divided into three stages: the classical era, which were lead by the reappearing of Mendelian genetics; the molecular era, which started with the discovery of DNA double helix structure; and the post-genomic era, accompanied with the first achievement of human genomics project. In each stage, the definitions of "gene" were totally different from each other. Especially in the post-genomic era, many scientists have redefined genes in response to the emerging scientific evidences; and all of them show the features of functional transition and decentralization. At the same time, non-genetic inheritance phenomena, such as regulatory factors and epigenetic inheritance, have attracted widespread attention and have even led to the debate on "new Lamarckism." It is foreseeable that genetics in the post-genomic era will overturn previous understandings of life mechanisms and influence various related fields.
The second chapter of this article focuses on the areas of evolution which are most directly related to genetics. Although initially Mendel's research was buried and nobody linked it to Darwinian evolution, after the rediscovery of Mendelian genetics in 1900, biologists working on statistical applications at once discovered the close relationship between the two. The "New Darwinism" based on genetics was established. The marriage of genetics and evolution became the "modern synthesize" of biology. The theory of genetics provided a solid microscopic foundation for the evolution of New Darwinism. Three evolutionary models in the 20th century were all based on genetic theory. However, at the end of the 20th century, the spontaneous view of nature that emerged from the field of complexity science impacted the classic theories of neo-Darwinism. Therefore, apart from the internal theoretical differences, the rise of "self-created Gaia" hypothesis, along with new genetic evidences in the post-genomic era, has become the problems which evolution scholars have to face with in the 21st century.
The third chapter discusses the issue of gene reductionism in genetics and evolution. Unlike general reductionism, gene reductionism is not a general discussion of material reduction or structure reduction, but a reduction of constituent information. In genetics, due to the aftermath of social Darwinism, there exists many misunderstandings in the discussion and application of gene reductionism. However, with the functional transition and decentralization in the post-genomic era, eugenics based on reductionism will inevitably replaced by the eugenics base on contextualism. In evolution theory, gene reductionism is mainly represented by Richard Dawkins' "Selfish Gene", which is a selection-level reduction theory. However, the term "gene" defined by Dawkins cannot be compatible with the newest genetics of the post-genomic era. The "meme" hypothesis derived from it is therefore even more problematic.
The fourth chapter extends to the debate on human nature based on genetics and evolutionary theories. Although social Darwinism was gradually abandoned by the academic community in the 20th century, the question of “seeking the natural basis for human nature” has never ceased. From the end of the 20th century to the present, several representative theories have become hot spots in the discussion of biology as well as sociology, including sociobiology, evolutionary psychology (abbreviated as ev-psych or EP), Darwinian Left, etc. Most of these theories were put forward by biologists, who used genes with hereditary and evolutionary characteristics as the natural basis of human nature. They tried to dissolve the classical dualism of "nature vs nurture (society)". However, due to the limitations of the pan-biological interpretation, their criticizes of dualism were forceless. On the other hand, the redefinition of gene in the post-genomic era has provided a new outlet for re-interpretation of the natural basis of human nature.
Finally, this dissertation summarizes several key conclusions by genetics and evolution studies at the beginning of the post-genomic era, and proposes the trend of shifting from gene centralism to contextualism. As gene expression instead of gene structure has become the focus of genetics, auxanology which promoted the shift from eugenics to eugenics, also proposed an indispensable perspective of the studies on inheritance phenomenon of genes as well as non-genes. At the same time, evolutionary developmental biology also combined auxanology and evolutionary studies. Unlike classical genetics and evolutionary studies in the 20th century, auxanology emphasizes the expression of genes in specific contexts, including the microenvironment of genes, the internal environment of organisms, and the external environment of nature and human society. Contextualism will very probably become the theme of the post-genomic era, which can bridge the dichotomy between nature and society, and providing a new perspective for explaining the essence of life.
Key words: gene; genetics; evolution; the Post-genomic Era
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