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Logic: Manner for wrting scientific papers (論理学)






Mount Usu / Sarobetsu post-mined peatland
From left: Crater basin in 1986 and 2006. Cottongrass / Daylily

Before talking about manner (that means predatory journal here) (はげたか雑誌)

Open Access

To publish research works on the Internet and make them available for free by everyone
Green Open Acess
final manuscript provided by institutional repository Ex. HUSCAP
Gold Open Acess
article processing charge (APC) after the acceptance

Predatory Journals

intend for only revenue from publication fee paid by authors

abuse of the business model for Open Access Journals

Their peer review is poor/inappropriate, or not done, and the quality of published papers is not guaranteed

APG, that is all!

I believe that every researcher knows I do not have to summarize predatory journals, such as all of the MDPI journals, any more.
Not to be involved in predatory journals
Know their features
Check the whitelists by the scholarly publishing industry

- Committee on Publication Ethics (COPE)
- Directory of Open Access Journals (DOAJ)

Check the scholarly literature databases which have selection criteria

- Scopus (Elsevier database)
- Web of Science Core Collection (Clarivate Analytics database)

Check blacklists

- Beall's List of Predatory Journals and Publishers
, and so on

Verify the metrics which the journals express by themselves

[Writing scientific papers, Natural sciences]

Before talking about manner (that means grammar here)

IMRAD (IMRAD)

Introduction, Methods, Results and Discussion

Introduction

Ten Steps to Writing an Effective Introduction
The purpose of the Introduction is to stimulate the reader’s interest and to provide pertinent background information necessary to understand the rest of the paper. You must summarize the problem to be addressed, give background on the subject, discuss previous research on the topic, and explain exactly what the paper will address, why, and how. Besides motivating a reader to read your manuscript and to care about your results, the Introduction is useful also to the journal’s reviewers and editors in judging the importance of your manuscript.
An Introduction is usually 300 to 500 words, but may be more, depending on the journal and the topic. Therefore, the Introduction needs to be very concise, well structured, and inclusive of all the information needed to follow the development of your findings.
Since every journal is different, it is important that you look at papers in your targeted journal to determine whether they use all of these steps. For example, some journals do not include conclusions in the Introduction.
  1. Begin with providing a concise background account of the problem studied
  2. State the objective(s) of the research that is the most important part of the introduction
  3. Establish the significance of your work: Why was there a need to conduct the study?
  4. Introduce the reader to the pertinent literature. Do not give a full history of the topic. Only quote previous work having direct bearing on the present problem
  5. Clearly state your hypothesis, the variables investigated, and concisely summarize the methods used
  6. Define any abbreviations or specialized terms
  7. Provide a concise discussion of the results and findings of other studies so the reader understands the big picture
  8. Describe some of the major findings presented in your manuscript and explain how they contribute to the larger field of research
  9. State the principal conclusions derived from your results
  10. Identify any questions left unanswered and any new questions generated by your study
Other points
  1. Be aware of who will be reading your manuscript and make sure the Introduction is directed to that audience
  2. Move from general to specific: from the problem in the real world to the literature to your research
  3. Write in the present tense except for what you did or found, which should be in the past tense
  4. Be concise

Methods

Methods

Results

Discussion (考察)

Expression of causal relation (因果関係表現)
Verb (動詞)
Lack of protein [causes, leads to, results in] mental disability.
Scurvy is a disease [caused by, resulting from, stemming from] lack of vitamin C.
Noun (名詞)
One reason why Xs have declined is that …
The causes of X are poor diet and lack of exercise.
A consequence of vitamin A deficiency is blindness.
Physical activity is an important factor in maintaining fitness.
Many other medications have an influence on cholesterol levels
Preposition phrase (前置詞句)
200,000 people per year become deaf [owing to, because of, as a result of, as a consequence of] a lack of iodine.
Conjunctive (接続語)
If undernourished children do survive to become adults, they have decreased learning ability. [Therefore, Consequently, Because of this,] when they grow up, it will probably be difficult for them to find work. The warm air rises above the surface of the sea, [thus, thereby] creating an area of low pressure.

Logic (論理)

s.l. The branch of philosophy concerned with the use and study of valid reasoning.
s.s. The study of logic features prominently in mathematics and computer science.

Symbolic logic (記号論理学)

ε-δ definition (ε-δ論法)
∀ε > 0, ∃m: n > m → |xn - a| < ε

∀, universal quantifier (全称記号)
∃, existential quantifie (存在記号)

= For any ε there exists a number m such that n > m implies |xn - a| < ε. or, For any ε there exists some number m such that n > m → |xn - a| < ε.

Tautology (循環論法)

circular reasoning, circular argument, vicious circle

A → → → → A

Correlation vs Causal relation (相関関係と因果関係)

Correlation relation

A weak claim - that variation in the independent variable is associated with variation in the dependent variable.
→ Chicken-and-egg

A ↔ B

pH-growth
Soil pH determines plant growth, or plant growth determines soil pH

Causal relation

A strong claim - that variation in the independent variable actually causes variation in the dependent variable.

A → B
Rain (precipitation → water level in a river
⇒ path analysis

Variable
Dependent variable: the target variable. The variable that is assessed as being the result of or predicted by other variables.
Independent variable (predictor): The manipulated variable. Variation in the independent variable is predicted to be associated with variation in dependent variable.

[statistics (統計学), meta-analysis (メタ解析)]

Ethics (倫理学)

= Moral philosophy (道徳哲学)
the branch of philosophy that involves systematizing, defending, and recommending concepts of right and wrong conduct
Ex. The Ten Commandments, classical ethics derived from Judaism
  1. You shall have no other gods before Me.
  2. You shall make no idols.
  3. You shall not take the name of the Lord your God in vain.
  4. Keep the Sabbath day holy.
  5. Honor your father and your mother.
  6. You shall not murder.
  7. You shall not commit adultery.
  8. You shall not steal.
  9. You shall not bear false witness against your neighbor.
  10. You shall not covet.
Classification
  1. Meta-ethics (メタ倫理学), concerning the theoretical meaning and reference of moral propositions, and how their truth values (if any) can be determined
  2. Normative ethics (規範倫理学), concerning the practical means of determining a moral course of action
  3. Applied ethics (応用倫理学), concerning what a person is obligated (or permitted) to do in a specific situation or a particular domain of action
    • Bioethics (生命倫理学), proposed by Jahr F (1926)
      need to integrate life sciences, biotechnology, medicine, politics, law and philosophy
    • Neuroethics (脳神経倫理学)
      ethics of neuroscience or neuroscience of ethics
    • Medical ethics (医療倫理学), grouped into professional ethics (職業倫理学)
    • Environmental ethics (環境倫理学)
    • Economic ethics (経済倫理学)
    • Information ethics (情報倫理学)
    • Animal ethics (動物倫理学): human-animal relationships and how animals ought to be treated
    • Others

Utiliarianism (功利主義) vs deontology (義務論)

Utiliarianism (功利主義)
Bentham, Jeremy 1748-1832, England

Greatest happiness of the greatest number

Mill, Stuart John 1806-1873, England
Deontology (義務論)
Kant Immanuel 1724-1804

Bioethics (生命倫理学, バイオエシックス)

Hippocrates (ancient Greek)

Hippocratic Oath (ヒポクラテスの誓い), written in Greek

Galenos

Environmental ethics (環境倫理学)

Research ethics (研究倫理)

FFP

fabrication + falsification + plagiarism

Nazi human experimentation
Tuskegee syphilis experiment

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