How to write a Paper?

Here are some tips and hints for writing a paper - most of these tips are also applicable for writing a thesis. Writing scientifically means also respecting a typical style. Here are some dos and don'ts in scientific writing (applicable independent from the idiom).
Another major problem of writing a paper may be the English - specially when you are not native English speaker (like me). Therefore here are some hints with scientific English rules and idioms.

How to start

Some general tips before you start to write a paper/thesis:
- Read other papers to get accustomed to the writing style and structure.
- Who is your audience? Do not try to impress your audience.
- Write in clear and concise sentenses and use adequate termini technici.

Strategy

- Organize your results. What is new/essential? What is the principal message?
- Review the primary scientific literature and compare your results with them.
- Start with the Introduction to get familiar with the theoretic background.
- Continue with the Methods and afterwards with your Results.
- Write the Discussion where you interpret and compare your results with others.
- Write the Abstract and the Title
- Finally self-revise carefully at least 2-3 times your own work before delivering.

Sections

Papers have a typical structure to which you should get accustomed. A thesis usually has the same sections, although in the Mexican(?) style you may find some "extra sections" like "Hypothesis" or "Justification".
- Title: Short and precise.
- Index (thesis only): for sections, figures and tables.
- Abbreviations (thesis only): Explanation of frequently used no standard abbreviations.
- Abstract: Short resume of your principal statement in the scientific context. Not more than 200-250 words.
- Introduction: What is the problem?
- Material & Methods: How did you solve the problem? This do not belong to the Appendice
and should include sufficient information for repeating the experiments.
- Results: What did you find out. Do not interpret the results (sometimes difficult).
- Discussion: What do your results mean (interpretation) - also in context to other publications.
- Acknowledgement (optional): Who helped (in minor parts).
- Literature: Cited literature within your work.
- Appendice (optional): Additional information.

In Spanish the sections are called: Título - Índice - Antecedentes (con hipótesis y justificación) - Metodología - Resultados - Discusión - Conclusiones (Resumen) - Bibliografía

Format

For the scientific community exist also a typical style or format how to present a scientific work. Usually past tense is used to describe procedures, observations and data (particularly Abstract; Material + Methods; Results) while own opinions and general conclusions or facts are written in present tense (particularly Introduction, Discussion). Here are some general tips:

Tables:

- A table present lists of numbers in columns and rows.
- Each table has a legend above, which explains briefly its content.
- All tables are numbered (Tab. #) and referenced within the text.

Figures:

- Scatter-, bar-plots etc. are usually used in black/white or greyscale.
- Graphs need the description of there axis with units and the symbols used.
- Photographs, diagrams etc. are figures. For photographs colour sometimes is indispensable.
- The resolution and contrast etc. has to be sufficient to reproduce it by standard photocopying.
resolution: 300 dpi for colour; 600 dpi for greyscale; 1200 dpi for line art
- Each figure has a self-explaining legend below.
- All figures are numbered (Fig. #) and referenced within the text.
- Processing of photographs (e.g. changing contrast, brightness etc.) is acceptable only if applied to all parts and to all controls in the same manner.

Abbreviations:

- Standard abbreviations, SI units or chemical structures should NOT be listed in the abbreviation list.
- Use abbreviation only if they are used for more than 3 times within the text.
- When appearing the first time in the work, introduce the abbreviation.
- For a thesis this may be repeated for each section.
- Afterwards the abbreviation has to be used!
- More detailled rules on nomenclature can be found at the IUBMB

Genes and Proteins:

	Human		Yeast		Bacteria
Gene abbr.	up to 6 up., ital., Lat. lett., Arab. num.	NUMB3	3 up., ital., Lat. lett.	ARG	3 low., ital., Lat. lett.	lac
Gene locus			follows Arab. num. up. = dominant low. = recessive	ARG2 arg2	follows up. Lat. lett.	lacZ
Gene mutation			hyphend Arab. num.	arg2-9	follows Arab. num.	lacZ139
Genotype superscripts			+ = wild type - = mutant, auxotroph R = resistance	ARG2⁺ arg2^- ZEO^R	+ = wild type - = mutant, auxotroph r = resistance	his⁺ his^- tet^r
Deletion			hyphend D, Arab. num.	ARG2-D1	Δ, gene locus	ΔlacZ
Insertion			X::Y (Y inserted into X)	arg2::LEU2	X::Y (Y inserted into X)	pyrC::Tn10
Protein abbr.	up to 6 up. Lat. lett., Arab. num.	NUMB3	3 Lat. lett., 1^st up. + p	Arg2p	3 Lat. lett., 1^st up.	LacZ
Phenotype superscripts			+ = wild type - = auxotroph R = resistance	Arg⁺ Arg^- Zeo^R	+ = wild type - = auxotroph r = resistance	His⁺ His^- Tet^r

pBR322	Plasmids low. "p" (indicating plasmid), up. Lat. lett., Arab. num. (not ital.)
CIAP Taq-polymerase HindIII Acc65I	DNA modifying enzymes low. Lat./Greek lett., Arab./Rom. num., not ital. (calf intestine alkaline phosphatase) when abbr. indicates genus & species, then 3 ital. Lat. lett., 1^st up. other lett./num., indicating the strain, is/are not ital.; the final Rom. num. indicates the number of enzyme found

up = upper case; low = lower case; ital. = italic
Lat. = Latin; Arab. = Arabic; Rom. = Roman
lett. = letter; num. = number

Latin names:

- The full name should be written out (Homo sapiens) the first time in the text and afterwards be abbreviated (H. sapiens).
- The genus name is ALWAYS capitalize (Homo).
- The specific epithet is NEVER capitalize (sapiens) - The entire name is always italicize.
- The common name can be used when the Latin name is given initially.

Units and Numbers:

- SI units should be used.
- Always use unit symbol when reporting numerical information. Never use a point to abbreviate these units.
- Unit symbols never have a plural-"s": 1 meter (1 m), 2 meters (2 m): ms would mean "millisecond"!
- ALWAYS put a space between number and unit: 1 m; 5 °C; 30 kJ
- For the pH, pI, pK_a the unit is placed before the number. Do not use words inbetween like "of": pH 7.0; pI 5.6
- In English the decimal separation mark is a point ("."), in Spanish a comma (","). Also in Mexico (NOM-008-SCFI-2002)!
- Always use the leading zero: 0.23 and NOT ".23".
- The symbol for multiplication should be "×" or "*" and not "•".
- Percent should be abbreviated by its symbol "%".
- The word "billion" should be avoided: this means in US-English 10⁹, in UK-English (formerly) 10¹², billón in Spanish is 10¹², as well as Billion in German is 10¹².
- Reporting statistics is (frequently) a special "problem".

Literature

It is important to cite correctly when you refer to outside sources of information (results, opinions). Write the important aspects in your own words (and NOT literally within parenthesis) and provide a reference as soon as possible afterwards - otherwise it would be plagiarism.
Here are some general citing rules, which applicate for journals in biological science. If you are writing for a concret journal, have a look for their citing style. Reference managers (e.g. Endnote) can help to change formats quickly.
- Cite only articles from trusty journals
- Cite only articles etc. which YOU have read.
- if you do not have access to an article make this clear in your citation, e.g. "according to the results obtained by XY (2001) and cited by AB et al." (2005) ..."
- Always keep the same style and no not mix citing styles.

Revision

Before submitting a paper to a journal, a proposal to a committee or a thesis to the tribunal it is very important to self-revise your own work. You have to check:
- The sequence of ideas has to be logic.
- Relationship between Introduction (what we knew before) and Discussion (how this work contribute/change this knowledge).
- A paragraph describes one topic and consists at least of 2 sentences.
- Correct use of termini technici.
- Remove colloquial or laboratory language.
- Remove all redundancy - i.e. do not repeat yourself.
- Check if you can say the same with fewer words (Brevity is the soul of wit).
- Read the text ALOUD: if it sounds strange, written will be more oddly.
Check also details - these kind of errors are annoying for the reader:
- Citations: Style, numbering, names, titles, completeness.
- Numbering of tables and figures.
- Line spacing, space between words, between numbers and units etc.
- Use spell check programs to find orthographic errors.

Journal

In times of populism and fake-news (e.g. Brexit or Trumpism) even the selection of the journal should be considered. The spirit of scientific research is that results and methods should be presented honestly and that a manuscript is reviewed by experts in the field previous to its publication (peer-review). This scientific tradition exists since more than 300 years and ensures that articles fulfill scientific quality standards and validity. This peer-review process makes the scientific method/work trustworthy.
Nowadays competition for (always too scare) resources (such as proyects, job positions etc.) is high and many times evaluation is based on the publication list of the researcher resulting in a typical ranking: the longer the better, which finally means "publish or perish". Thus, recently many new pseudo-scientific journals (aka Predatory Journals) emerged, where you pay for publishing (justified as open access) and which appear to be scientific but they do not meet scientific standards because they lack the mandatory peer-review process. To publish in or cite those kind of journals will discredit first of all youself and your own work and on the long run even the credibility of the scientific community.

So be aware of Predatory Publishers and their Predatory Journals, which frequently use misleading impact factors. Sometimes they use very similar names to recognized journals (Hijacked Journals).

The original site with a list of predatory journals from the Librarian Jeffrey Beall was shut down in January 2017.
An alternative for the Beall's list of predatory journals is the Norwegian Register for Scientific Journals, Series and Publishers NSI, which differentiate between "level 2" (highest rating, top 20%), "level 1" (normal rating, top 80%), "level 0" (lowest rating, non-academic) and "level X" (dubious or possibly predatory).

Trustful is, for instance, the "International Association of Scientific, Technical and Medical Publishers" and their STM-members. On the other hand, not all publishers with Article Publication Charges (APC) are predatory journals; to be sure, check if they are listed in the Directory of Open Access Journals. At least the journal should be member of COPE, the Committee on Publication Ethics.

Last modified: 16.02.2022