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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

Data paper (データ論文)
= data description paper

Objectives: data sharing and reuse

Ex. Scientific Data, Date in Brief    ☛ Data paper

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

APC, that is all the predator needs!

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
- Think, Check, Submit, 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.

☛ 引用と盗用

Citation 引用

When citing a reference, focus on the ideas, not the authors.

It is important to cite sources in the introduction section of your paper as evidence of the claims you are making. There are ways of citing sources in the text so that the reader can find the full reference in the literature cited section at the end of the paper, yet the flow of the reading is not badly interrupted.
It is important to cite sources in the discussion section of your paper as evidence of the claims you are making. There are ways of citing sources in the text so that the reader can find the full reference in the literature cited section at the end of the paper, yet the flow of the reading is not badly interrupted (see also Introduction).

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.
Formal and informal logic
Formal logic (形式論理): focuses on deductively valid reasoning, where conclusions necessarily follow from premises based on structure alone
Informal logic (非形式論理): deals with reasoning in everyday language, including argumentation and fallacies

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.

Paradox (パラドクス)

Def. A statement or situation that leads to a contradiction or defies intuition, despite seeming logically sound

often the result of self-reference, circular reasoning or inconsistencies within a system

Self-referential paradox (自己言及のパラドクス)
Ex. The Liar Paradox: "This statement is false."

Tautology: if the sentence is true, then what it asserts must hold—that is, it must be false. But if it is false, then it must be true

Ex. The Grelling–Nelson paradox (グレリング=ネルソンのパラドクス):

autological (自己記述的): adjective describes itself

Ex. "short" is short.

heterological (非自己記述的): adjective does not describe itself

Ex. "long" is not long.

Q. "Is the word 'heterological' heterological?"
A. If it is, then by definition it should not be; if it is not then it should be. The self-referential twist of applying a property to its own descriptor leads to a contradiction

Ex. The Berry paradox (ベリーのパラドクス): Ex.

"the smallest positive integer not definable in fewer than 11 words"
→ this paradox deals with definitions
The definition itself appears to define that number in fewer than 11 words, which is a contradiction. The paradox is rooted in the self-referential aspect of attempting to define a term by referencing its own definability

Ex. The Barber paradox (理髪師のパラドクス): ☛ Russell's paradox

Ex. A barber who shaves those people who do not shave themselves

Q. Does the barber shave himself? → contradiction

If he does, then according to the rule, he should not shave himself. If he does not, then he qualifies to be shaved by the barber
the trouble that arises when a rule or definition refers back to itself
☛ associated with set theory

Paradox of Zenon (ゼノンの逆理)
= Zeno's Paradoxes
The paradoxes of motion (deny the presence of motion)

Dichotomy paradox
Achilles and the tortoise
Arrow paradox
Paradox of place
Paradox of the grain of millet
The moving rows (or stadium)
(these have been solved)

Syllogism (三段論法)

A → B, B → C ∴ A = C

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 and Mill
Deontology (義務論)
Kant Immanuel 1724-1804

Bioethics (生命倫理学, バイオエシックス)

Def. the study of philosophical, social, and legal issues in new discoveries and techniques in biology, e.g., genetic engineering and the transplantation of organs
Hippocratic Oath (ヒポクラテスの誓い), written originally in Greek
I swear by Apollo Healer, by Asclepius, by Hygieia, by Panacea, and by all the gods and goddesses, making them my witnesses, that I will carry out, according to my ability and judgment, this oath and this indenture.
To hold my teacher in this art equal to my own parents; to make him partner in my livelihood; when he is in need of money to share mine with him; to consider his family as my own brothers, and to teach them this art, if they want to learn it, without fee or indenture; to impart precept, oral instruction, and all other instruction to my own sons, the sons of my teacher, and to indentured pupils who have taken the Healer's oath, but to nobody else.
I will use those dietary regimens which will benefit my patients according to my greatest ability and judgment, and I will do no harm or injustice to them. Neither will I administer a poison to anybody when asked to do so, nor will I suggest such a course. Similarly I will not give to a woman a pessary to cause abortion. But I will keep pure and holy both my life and my art. I will not use the knife, not even, verily, on sufferers from stone, but I will give place to such as are craftsmen therein.
Into whatsoever houses I enter, I will enter to help the sick, and I will abstain from all intentional wrong-doing and harm, especially from abusing the bodies of man or woman, bond or free. And whatsoever I shall see or hear in the course of my profession, as well as outside my profession in my intercourse with men, if it be what should not be published abroad, I will never divulge, holding such things to be holy secrets.
Now if I carry out this oath, and break it not, may I gain for ever reputation among all men for my life and for my art; but if I break it and forswear myself, may the opposite befall me. (Translated by WHS Jones)

☛ research ethics (研究倫理)

Environmental ethics (環境倫理学)

Researching the moral relationship of human beings to, and also the value and moral status of, the environment and its non-human contents
Competing paradigms =

Anthropocentrism (人間中心主義) vs.
Physiocentrism (ecocentrism, 環境中心主義/自然中心主義) vs.
Theocentrism (神中心主義)

Research ethics (研究倫理)

FFP

fabrication + falsification + plagiarism

Nazi human experimentation
Tuskegee syphilis experiment

Fraud/fabrication
Ex. Piltdown hoax (ピルトダウン事件) in anthropology
≈1909 Dawson, Charles (1864-1916, England)

lawyer and amateur archaeologist
nickname: "Wizard of Sussex" (Sussex Daily News) discovered a fossil in Piltdown near Uckfield, England

1911-1913 Dawson C: additionally discovered fragments of bones

cranial bone, chinbone and teeth

1913 Woodward, Arthur Smith & Dawson C

the fossil named Eoanthropus dawsoni
billed as the missing link between humans and other great apes

1915 Dawson C: cranial bone and molars, 3 km far from Piltdown
1915 Miller Jr, Gerrit Smith: scepticism about the Piltdown find
1950 Oakley, Kenneth P: fluorine-dating

younger than any other fossils sampled from Piltdown (50 Kya)
fabricated canies of young ape
artificially-colored surface

1953 Oakley KP, Wilfrid Edward Le Gros & Weiner, Joseph

concluded that Piltdown Man is a forgery

human skull in medieval age +
orangutan lower jaw in 500-year-old +
chimpanzee teeth of fossil

1953-1955 Keith, Arthur (1866-1955, UK): revelation of Piltdown fraud

When the fossil was reported, he supported the findings

Ex. Clone mouse (クローンマウス)
1968 Illmensee: nuclear transplantation, fly

exchanged the nucleus of an unfertilized egg with a nucleus from a fertilized egg

1981 Hoppe & Illmensee: nuclear transfer, commonly-called clone mouse

trumped-up charge - difficulties in replication study

1983 Bürki: accused Illmensee of falsifying data
Ex. gene recombination (遺伝子組換)
1973 Cohen SN & Boyer HW: established gene recombination technique
1973 Berg P: considering the risks linked to recombinant DNA techniques

NIH guideline: negative inhibition → positive control

Identity of the forger
2003 Russell, Miles (Bournemouth University): re-examined the fossils

over 38 specimens are fabricated

2016 De Groote et al.: using DNA analyses + morphometric analyses

the consistent method and common source - the work of one person
= Dawson

  • De Groote et al. 2016. New genetic and morphological evidence suggests a single hoaxer created 'Piltdown man'. Royal Society Open Science 3, 160328
HARKing
= Hypothesizing after the results are known (Kerr 1998)
THARKing: transparently hypothesizing after the results are known (Kerr 1998)
CHARKing (or Pure HARKing): constructing new hypotheses after the results are known and presenting them as a priori hypotheses
RHARKing: retrieving old hypotheses from the existing literature after the results are known and presenting them as a priori hypotheses (Rubin 2017)
SHARKing: suppressing a priori hypotheses after the results of tests of those hypotheses are known
+ Active and passive HARKing
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