Month: February 2016

How to write a research paper


Dr. Guido David hosted his annual research paper writing seminar yesterday. I was supposed to attend last year but I was uninformed of the schedule for some reason. Fortunately I was able to create my thesis paper simply by observing the format of several thesis papers of graduates and with some guidance from him. Being a professor who produces scientific papers for a living, he insists that years of experience merits him enough credibility to give a lecture on it, haha. Anyway, for the benefit of students who weren’t able to attend the seminar, and for those who want to have a general idea of the research paper writing process, here are the main points of his talk (made 1000% more fun with some writing humor and my go-to gallery of academic woes, PhD Comics).


  • Thesis/dissertation
  • Research proposal
  • Journal publication
  • Conference proceedings


  • In full detail: in-depth literature review, definitions & description of all formulas, even basic ones used in the study
  • Around 40-100 pages, self-contained (built with necessary background, so that even lay-academics can grasp it)

Research Proposal


  • Proposal for research funding
  • Includes only the most important parts (problem statement, objectives, clearly-outlined methodology, significance, etc)
  • The investigator must prove that he/she knows how to approach the problem and has a clear plan (i.e., the research grant will not be wasted). Preliminary results are helpful.
  • Contains brief related literature review (what has already been done about the problem/using the method) -> put everything very related or similar to your work
  • Required for masters and dissertation

(Scientific) Research Paper

  • New results. Publication-worthy. Content/findings must be strong enough
  • Concisely written. Well-known results/technologies/models should not be explained. Even derivations may skip details.
  • Usually 5-10 pages, sometimes more (for full research paper)

Conference Proceedings

  • Same parts as research paper
  • Not as strong/in-depth. Meant for laypersons in the field


  • Title
  • Abstract
  • Introduction
  • Methodology
  • Results & Discussion
  • Conclusion


  • Concise, describes research well enough, distinguishes it from other studies/papers on the same topic
  • Title is specific enough (which model is used, the exact problem being solved)


  • The searchable part/quick description of the paper, 200-300 word limit
  • Includes:
    • Brief introduction of concepts (1-2 sentences)
    • Short overview of methodology
    • Summary of major results
  • If topic is obscure/not well known, terms must be defined


  • Defines the problem, significance of the study, scope & delimitation
  • Background of the study: brief review of relevant literature to highlight the distinguishing features of the present study. usually just 1-2 paragraphs on relevant lit.
  • Necessary terminology is defined
  • Significance: from a scientific standpoint (you’re contributing new knowledge), not necessarily in terms of societal contributiondone.png
  • Scope: limitations of the paper, restrictions of the models, assumptions
  • Theoretical framework: methods/theorems that are fairly well known (but not well known enough to be excluded)


  • Defines steps/approach to solving the problem
  • Most applicable to empirical/experimental studies
  • May use equations/theorems that lead to your main problem

Results and Discussion

  • Include most important results
  • Graphs, plots, figures, tables are the preferred way of presenting multiple data
  • Highlight findings that are new or surprising. Discuss in sufficient detail.
  • If thesis: you can put as much non-redundant results as possible
  • Captions: under figure, above table


  • Repeat most important parts of the study. Include significant findings, pioneering techniques or methods
  • Highlight limitations & future work (extensions)


  • Avoid Wikipedia & other online references not based on publications (no accountability or authorship, could’ve been edited by anyone)
  • References should be in the prescribed format (APA, MLA, etc.)
  • Refer to books and articles from research journals. Unpublished research articles/personal communication may be included too if based on a relatively new topic

Extended Abstract

  • Condensed thesis as guide for the examiner, with preliminary results (deadline usually on defense week)
  • Intro usually not in past tense. Result is never in future tense.



Before anything else, here’s a useful infographic I found about plagiarism. Pretty scary. D:



  • Never copy-paste. Quoted phrases that are cited are acceptable but usually not used in scientific papers
  • Paraphrasing other papers without citation is considered plagiarismselfplagiarism.jpg
  • Do not plagiarize even your own work (self-plagiarism)
  • Safest way to go is to always cite sources
  • Tip: read something, put it down, write from memory and own understanding (your writing will formulate itself!)

Writing Flow

  • Don’t start with introduction. It will give you writer’s block.
  • Start w/ methodology (try to connect the equations and theorems used ) & results (numerical results, plots, derivations, etc) first.
  • Write in a very factual and formal way.
  • A boring way of writing is okay. It’s not a crime, lol
  • Keep tense consistent.
    • Scientific papers: usually all in past.
    • Thesis: intro & method in present, results & conclusion in past (his general approach)
    • Intro & methodology could be in future
  • After methodology & results, write the intro. Since there are already results, you should have a better idea on which objectives & significance you want to emphasize in the study.
  • Define relevant terms that aren’t general knowledge in the field
  • Review of related literature should be short. Stick to the most relevant references.
  • Write the conclusion. highlight important results. by describing the limitations, you already propose how the study can be extended.
  • Write the abstract last. Compress entire paper in one paragraph, should be readable from layman’s perspective
  • Doesn’t necessarily present results, just mention that the paper was successful was successful in obtaining results.
  • No citations & related lit. No equations.


  • Spell-check it, have it proofread
  • Note: not explaining well/writing well could be grounds for rejection of paper
  • Write formally. No shortcuts (&, etc) and abbreviations/acronyms should be defined
  • Numbers 1 to 10 must be written in words, unless numerical value is being highlighted
  • Concise but clear and factual. remove unnecessary lines, words, or redundancies.
  • Avoid vague words that serve no purpose (e.g.: The process was quite fast. The thing that was most relevant…)



Choosing a journal for publication

  • If high quality work, try high quality journals (known in the field)
  • Index of journals: Scopus, Thomson Reuters, etc
  • Local: Matimyas, Phil. Journal of Sciences(?), Phil. Computing Journal(?), etc
  • Multidisciplinary work: choose where the work will be more appreciated (e.g.: for math finance work, submit to applied math journals)
  • Try the journals where the papers you referred to were published

Condensing Thesis to Journal format

  • Include very main result. Choose representative values for multiple similar data
  • Ask adviser to help you remove inessential stuff (most likely what I’m going to do, haha)
  • Paraphrase your own writing!


  • 20-40 is a good number for research papers. (thesis papers usually around 10)
  • Shows that the author did their homework and are very familiar with the topic

    How NOT to write a research paper


I’ll work on transforming my own thesis into a journal submission soon. I hope I’m ready! XD

Indirect Mentors

I often wish I had someone to give me solid guidance throughout the intricate process of growing up. I’m grateful that my parents provide me with the necessities of life while I still can’t, but I’m not close enough with them to be able to pour out my heart. I don’t have any older brothers/sisters who could give me their intimate “been-there-done-that” lessons. I’ve had mentors but they prefer to share just their technical knowledge and help me with my career alone, so I am still left to my own devices when it comes to my personal growth. I’ve been this way since high school, like a child still learning to internalize what’s right over wrong, the weight of my decisions increasing with time.


Over time, I had built a sketchy system for going through the motions of daily life, which was usually either monotonous or in stasis due to an emotional disaster that I don’t know how to deal with. I graduated twice with good credentials but I felt mediocre and pathetic, and I didn’t understand it. When the most recent emotional disaster shook my core and broke my once solid trust in friendship, I would have attempted to take my own life, if not for my therapist who reminded me (in a straightforward, rational way) that it’s not worth it since I still have so much to look forward to and so much to offer the world (not to mention, so many caring people to leave behind).

I gave myself a long time to reflect on my life, and then it occurred to me: I really have to rise up above my current self. I needed some sort of compass for personal development. So to have the kind of guidance I think I need, I decided to outsource wisdom from the internet, fiction, and my observations/eavesdropping.

I subscribe to the business and life lessons imparted by three entrepreneurs/authors who have proven themselves successful for changing their life, changing other people’s lives, and changing the world: Mark Manson, James Altucher, and Jay Samit. Everyday I pick up ideas from their writing and podcasts that stick to me enough that I use them to improve my philosophy. (The best part is, I can always reach them via email! And I did.)

I draw inspiration from the fictional characters I grew up with. Kazuma Azuma for his ingenuity, Beatrice Ushiromiya, Light Yagami, and Miles Edgeworth for their confidence, the gamers Shiro, Sora, Keima Katsuragi, and Umaru for beating every game, Shinichi Chiaki for overcoming his deep-rooted phobia, and all the Kuuderes for their calm and collected yet competitive disposition.


Nodame and Chiaki, from the series Nodame Cantabile

Now that I think about it, I should also be grateful to have crossed paths with a few notable people throughout the course of my life.  Heck, some of them aren’t even close to me or probably aren’t aware of my existence, but a great part of me was forged from what I learned from them.

  • My grandmother’s countless stories about rising up from poverty constantly remind me of the importance of willpower, hard work, education, and generosity.
  • Nory (my scholar)’s continuing excellence over her struggles in life taught me the importance of allocating one’s resources efficiently.
  • Kwez (with whom I shared a gaming circle) and his love and mastery of games ignited my passion for Game Theory.
  • Nina (my cosplay partner) made a strong impression the night I met her, by staying optimistic about life and focusing on her dreams in spite of all the things that recently happened to her that could crush anyone’s soul.
  • Ian B. (the only other INTJ I personally know)’s circumstances in life made me realize the significance of the adage “It is important to stand up for yourself, even if it means standing alone”.
  • Dr. Custer (the main guy of Pinoy Scientist)’s undying enthusiasm about pushing forward any idea he can think of and pushing people to make progress inspires me to be passionate about my endeavors.
  • Daniel (the guy who taught me how to play bridge/resistance and configured the LaTeX editor on my laptop)’s definition of excelsior manifests in the way he carries himself, and it strongly reaffirms mine.
  • Through his dealings with me, Dr. Guido (my current mentor) showed me the importance of open-mindedness, adaptability, and maintaining a rational perspective during the toughest of times.
  • And thanks to Dara (one of my closest friends), I learned the necessity of finding oneself and emotional independence, the hard way.

These people are influential not for any advice they have given me, but for what I choose to make out of and internalize from my observations and experiences with them. Now I am more confident, resilient, and in a higher existence than my yesterday’s self.

I guess, at the end of the day, only I am responsible for my own growth and development as a person. That I can impart wisdom on myself that I may not be able to get anywhere else. That even if I don’t always recognize it, I myself am my own mentor.


Interview with Jeffrey Beall (On predatory journals and digital age librarians)

For a Pinoy Scientist episode, our group (w/ Dr. Custer and Dr. Guido) interviewed Dr. Jeffrey Beall, the creator of Beall’s List, through a video conference. I honestly had no idea who he was or what the significance of his initiative is (or even how his name was spelled, haha) beforehand. But I did overhear that it is a controversial topic in the scholarly environment, and since I am to forge an unorthodox path to the academe, I figured that this is something worth knowing. Here is what I picked up from the interview:


Dr. Jeffrey Beall is an academic librarian who pursued degrees in Spanish, English, and Library Science. (According to him, Library Scientists deal with the curation of learning resources, information retrieval, and optimizing the research environment.) He has 25 years of library work under his belt, first in Harvard for 10 years before moving to the University of Colorado Denver.


His biggest contribution to the academe is a blacklist of journals. The 900 or so publishers in Beall’s list are said to be mostly predatory or hijacked (or just plain sketchy). He defines predatory journals as those that take advantage of the Gold open access model in an unethical manner. It is quite normal for some journals to charge a publication fee from the author, but the main issue against predatory journals is that this business model can be exploited to prioritize the revenue without regard for the quality of the papers they accept. Hijacked journals, on the other hand, are journals the general look and feel of which were counterfeited from legitimate journals to deceive authors into publishing there instead (evil twins!).

Some of the criteria he uses to judge whether a journal deserves to be in the list are:

  • dishonest/unhealthy peer review
  • spammy (spelling, grammar, math mistakes)
  • lesser known but looks strangely familiar
  • easily accepts papers or promises rapid publishing (too good to be true!)

Beall continually maintains his list through feedback (it’s said to be currently in its 3rd edition) and notifies people of recent additions through his blog and twitter. What makes it controversial is that some of the items in his blacklist also belong to some existing whitelists. For example, I found out from Nature that he took some heat for adding Frontiers (reason: publishing 2 pseudoscientific articles, deeming its standards questionable) to his list despite its reputation for being a well-patronized journal. Some scholars try to discredit his list (and even give lawsuit threats they never really act on, haha) and accuse him of basing it purely on his intuition, but in my opinion, one should not disregard intuition in quality control since it could be the only way to detect intricate deceit (or expertly-disguised stupidity) hiding behind flawless logic.

Fortunately, the most of the feedback he garners are positive. There’s no doubt that academia needs journal police like him to protect researchers all over the world from falling prey to predatory journals.

Some advice from Beall to people who are starting out on their academic career:

  • Citing articles from predatory journals is risky. Taking advantage of them for tenure will most likely compromise credibility.
  • Take whitelists and blacklists with a grain of salt.
  • Publish in good journals. They don’t have to be top journals, as long as they’re high-quality.


The onset of the digital age brought about an obvious change in learning media. Most information are now online, but Beall says that does not mean less people read books nowadays — they simply switched from print to ebooks. Thanks to that, the role of librarians have evolved as well, from being simply custodians of books to being pioneers in improving access to and adding value to information. According to him, the electronic environment also makes a librarian’s life easier, as it automates the process of search and lending. And of course, they have an easier time with helping researchers.

[Fun fact: There are more libraries that McDonald’s branches in Denver. Unlike in the Philippines. XD)



Dr. Custer likes shining light on the human side of scientists. Dr. Beall is no exception, so here are some things about his personal life:
  • He likes reading books about volcanoes, nature, and astronomy, but he hasn’t had enough time to read lately.
  • He also likes driving to mountains (Denver is a mountainous region, after all).
  • Being a single man, he finds joy in traveling for academic talks.
  • His website is self-maintained and he has no time to collaborate (Dr. Custer has a habit of offering a collaboration to guests, haha).

Zika Virus, Philippine context

Today I have been invited as a representative of Pinoy Scientist (together with Dr. JD) to attend a press forum on the Zika Virus, a hot topic within the scientific community and recently a cause for concern among Filipinos. Present to give reliable information and answer any questions were Dr. Lyndon See Suy (Spokesperson of the Department of Health) and a representative of the Philippine Society for Microbiology and Infectious Diseases (I didn’t catch his name, unfortunately).


Zika Virus forum

The Zika virus has been discovered many years ago but it is only now that it is causing widespread worry due to it being transmitted by the same type of mosquito that carries dengue (Aedis aegypti, abundant in the Philippines) and a recently discovered strong correlation between microcephaly (smaller cranium and brain size due to underdevelopment) and pregnant women infected with the virus. A case of Zika virus infection in the Philippines has been reported but how that person contracted it is still unidentified.


Fast facts about the Zika virus

I learned that the symptoms manifested by persons who contracted the Zika virus are almost the same as those of dengue, but the main difference is that Zika virus causes conjunctivitis while dengue’s uniqueness lies in the high fever and rashes. The DOH and PSMID spokespersons maintain that dengue is still the scarier one to have but the Filipinos should not be complacent about the mildness of the symptoms of the Zika virus either. According to them, the Zika virus is hard to detect or contain because around 75% of those who have the virus show no manifestations at all, and that makes it hard to put definite travel advisories (except maybe for pregnant women) and to check returning tourists and overseas Filipino workers.

The main agenda for the near future is to encourage further research, disseminate reliable information, and prevent unnecessary panic. The government agencies concerned call for the action of the community as well in reducing the chances of spread of the virus in the Philippines by practicing sanitation and destroying potential mosquito habitats. They also hope that by the time the Filipino athletes would have to participate in the World Cup in Brazil, the newest discoveries and technologies would help give them some sort of protection.

So far, there is still a great need for conclusive results (a correlation does not imply causation, no matter how strong it is). Most of the information we have to know to protect the susceptible and cure the infected remains to be discovered.  That being said, everyone is advised to stay tuned to the developments in the worldwide Zika virus research. Viruses evolve and humanity must keep up to ensure survival, and here lies the importance of science and technology research.


Dr. Lyndon See Suy and the Pinoy Scientist representatives


EDIT: Here is Dr. JD’s poem about the press forum:

Zika poem

PSG Updates

The three Pinoy Scientist hosts regularly have meetings, but this time they decided to involve me (that, or Dr. JD just really wanted me to have a taste of her cooking). Dr. Guido told me that they’re creating a corporation out of the program and are including me as one of the members. I don’t know how it works yet, I mean I obviously can’t contribute anything monetary, but I’m very excited about being acknowledged as an official member of their group. 🙂 I’ll get to pitch in some value-adding ideas that have the potential to improve (and possibly reshape the contours of) the Filipino scientific community, just like any of Dr. Custer’s ideas. And I’ll be able to learn a lot from them, yay! It’s great to be able to expose myself to the role models I need. 🙂