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My JE dictionary gives me "system" for the definitions of both 組織 and 体系. Are these two words wholly synonymous, and if not, how are they different? In addition, is there a difference between 組織的(な) and 体系的(な)?

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組織 and 体系 are usually not interchangeable.

The primary translation of 組織 is "organization", and it usually refers to a group of people (community, cooperation, association, etc) at least in modern Japanese. It also refers to animal "tissue" (muscle, vessel, gland, etc). 構成 is the word that is usually used to refer to a configuration/construction of a mechanical system.

体系 is "(whole) system", and is a big word that primarily refers to a whole hierarchy of knowledge/rules/systems in a certain field. Use this word only for something very big and complex. For example 法律の体系 (or 法体系) refers to a whole legal system of a certain country.

Likewise, 組織的な is "organized" (as opposed to "savage" or "uncontrolled") or "on an institutional basis" (as opposed to "personal"), whereas 体系的な is "systematic" (as opposed to "individual" or "random"). 体系的に英語を学ぶ means "to learn English systematically", i.e., like going through a large textbook from page 1. 組織的に英語を学ぶ would usually mean members of an organization learn English together by the order of a boss.

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Consider the definitions from daijirin:

組織

(1) 組み立てること。また,組み立てられたもの。「所謂劇を―する要素は何か/神秘的半獣主義(泡鳴)」

(2) 特定の目的を達成するために,諸個人および諸集団に専門分化された役割を与え,その活動を統合・調整する仕組み。または,そうして構成された集団の全体。また,それを組み立てること。「会社―」「社会―」「組合を―する」「議会を―する」

(3) 生物体を構成している単位の一つで,同一の機能と構造とをもつ細胞の集団。動物では,上皮組織・結合組織・筋肉組織・神経組織,植物では分裂組織・永久組織などに区別される。

(4) 構成鉱物の大きさ・形・並び方などによる岩石の内部構造。石理。

(5) 織物で経(タテ)糸と緯(ヨコ)糸を組み合わせること。また,その交錯のし方。「織物―」

体系

(1) 個々のものを秩序づけて統一した組織の全体。

(2) 一定の原理に基づいて構成され,内的整合性をもっている科学的あるいは哲学的命題の集合。システム。系。

My attempt to tl;dr this:

組織 = bunch of things getting together (eg: an organization of people)

体系 = what gives order to a whole 組織.

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