References

- Metaphorigins Instagram Page - https://www.instagram.com/metaphorigins/
- Wikipedia - Scientific Literature - https://en.wikipedia.org/wiki/Scientific_literature
- Wikipedia - Academic Publishing - https://en.wikipedia.org/wiki/Academic_publishing
- Geocentrism vs. Heliocentrism - https://www.youtube.com/watch?v=RsKdoEtZdd8
- Ptolemaic System - Article - http://abyss.uoregon.edu/~js/glossary/ptolemy.html
- CNN Poll - https://www.cnn.com/2010/TECH/03/01/social.network.news/index.html
- SciShow - https://www.youtube.com/user/scishow?app=desktop
- Smarter Every Day - https://www.youtube.com/user/destinws2
- ASAP Science - https://www.youtube.com/user/AsapSCIENCE
- Argument from Authority - Fallacy #9 - https://plato.stanford.edu/entries/fallacies/#CorFal
- Wikipedia - Global Warming - https://en.wikipedia.org/wiki/Global_warming
- Proximal Origin of SARS-CoV-2 - Second Link - https://www.nature.com/articles/s41591-020-0820-9
- A Review of SARS-CoV-2 and the Ongoing Clinical Trials - Fourth Link - https://www.mdpi.com/1422-0067/21/7/2657
- Scopus - Database - https://www.scopus.com/home.uri
- Web of Science - Database - https://clarivate.com/webofsciencegroup/
- Google Scholar - Search Engine - https://scholar.google.com/
- PubMed - Database - https://pubmed.ncbi.nlm.nih.gov/
- Database Searching Techniques - University of Michigan - https://www.youtube.com/watch?v=Ccw387GoA1k
- Average Reading Speed - https://irisreading.com/what-is-the-average-reading-speed/
- Catalogue of Scientific Papers - https://www.nature.com/news/the-catalogue-that-made-metrics-and-changed-science-1.22961
- Structure of a Scientific Paper - https://guides.library.illinois.edu/c.php?g=348214&p=2346645
- Reading a Paper - Dr. Pete Carr - https://www.youtube.com/watch?v=IeaD0ZaUJ3Y
- Dr. Gordon Rugg - Article - https://www.keele.ac.uk/discover/news/2020/january/academic-writing/can-be-boring-reasons.php
- Double Blind Randomized Clinical Trial - Article - https://www.jclinepi.com/article/S0895-4356(00)00347-4/fulltext
- Dr. Daniel Oppenheimer - https://onlinelibrary.wiley.com/doi/abs/10.1002/acp.1178
- Ig Nobel Prizes - https://www.improbable.com/ig-about/
- Wombat Poop - http://meetings.aps.org/Meeting/DFD18/Session/E19.1
- How to write a first-class paper - https://www.nature.com/articles/d41586-018-02404-4
- Why academic writing stinks - Dr. Steven Pinker - https://stevenpinker.com/files/pinker/files/why_academics_stink_at_writing.pdf
- A guide to peer review in ecology and evolution - https://www.britishecologicalsociety.org/wp-content/uploads/Publ_Peer-Review-Booklet.pdf
- Dr. Richard Pearson - Lecture - https://www.youtube.com/watch?v=gJ_Yxeh9Olk&t
- Proof that 1 + 1 = 2 - http://mathforum.org/library/drmath/view/51551.html
- New article - https://www.kjbmercurio.com/masters
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- Creative Commons Attribution 3.0 Unported License | https://creativecommons.org/licenses/by/3.0/deed.en_US
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Transcript
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To my pulchritudinous family and friends. Near and far. Old and new. This is Kevin Mercurio on the mic. And welcome to the tenth episode of the Metaphorigins Podcast.

After a small hiatus, I have returned! For one more episode of the season. I honestly didn’t realize how much fun I would have doing these, as I was filling in time between the end of my Masters and the next adventure. I will be continuing with a second season for sure.

To show support if you like this sort of content, please make sure to rate and subscribe to the podcast on Apple or whatever platform you are listening to this on, and follow @metaphorigins on Instagram, where I will be posting most of my updates, as well as on my personal website: kjbmercurio.com/metaphorigins. For regular listeners of this podcast, you may have noticed the new customized Metaphorigins t-shirts on the Instagram page. This is the new item which I I will be giving away to one lucky listener, right now! I have performed the draw for the butterfly-printed Metaphorigins shirt, and the winner is Belinda Briones. Yaaaay! Congratulations! I’ll shoot you a message following this episode.

I really appreciate the support I’ve received from this. I will host more giveaways in the new season starting sometime in July, so stay tuned for that. And thank you so much.

Okay, In today’s episode I’ll be taking a break from the imaginative reality of metaphoric wonders and do something similar to this season’s fifth episode. That’s right. Today, I will try my utmost best to discuss with you, in the most intriguing and creative way possible, a topic that everybody not only working in science has experienced, but now almost everyone in the world has familiarity with due to global problems like climate change and infectious disease… That topic is scientific literature.

What do I mean about scientific literature? I don’t mean the buzz-worthy articles that we see in mainstream news sites or reported on 24 hour news shows. However, these stories usually arise after a landmark scientific discovery has been made public. I don’t mean the widely interesting science books you can purchase at your local bookstore. Though, these books usually reference true scientific literature. No. I’m talking about scientific articles that are published in credible scientific journals by notable scientific personnel reviewed by anonymous scientific experts. I tried my best to fit the word scientific as many times as I could in one sentence.

To my science pals, of course you know what I mean by scientific literature. You’ve been engrossed in it since the beginning of your journey, likely in undergrad but possibly later in your career. You’ve prepared your projects by reading it, you’ve adapted your methods by citing it, and hell, you’ve thought critically about your western blot or algorithm because of it. So defining true scientific literature is simple, right? I’ll get back to you folks in a bit.

To my non-science chums, I want to be clear that I don’t know whether there is a correct definition for scientific literature. Wikipedia describes scientific literature as, “compris[ing] scholarly publications that report original empirical and theoretical work in the natural and social sciences, and within an academic field…” It also introduces a separate term, Academic publishing, described as “the process of contributing the results of one's research into the literature, which often requires a peer-review process.” Therefore scientific literature is the result of academic publishing of scientists’ research.

Why exactly am I stressing its definition so much? I’ll tell you why. We often think that the knowledge we hear about in daily news, saturated by thousands of books, newspapers, websites, TV channels, radio or podcast broadcasts, and even scientific literature itself, are true. But it is filtered. To get a little philosophical here, we are living in a subjective reality of facts. Scientists, politicians, journalists, or we ourselves base our knowledge on what has been written to be correct and defined in scientific literature. What gets defined as scientific literature, what we deem as fact, is actually a personal take on describing the physical and natural world, reviewed by a finite amount of other people. These people will always have biases. And it is the ethical value of any one person in this chain to ensure that bias is reduced as much as possible and the conclusion derived from observation and experimentation still hold true. Side note, the only exception to this may be the field of mathematics, almost like a language that can theoretically describe everything.

Let’s stay on track though. Again, I stress this because the idea of fact derived from scientific literature is flawed. In other words, the fact that what you read in an article written by a journalist who read a scientific journal’s summary of its recent scientific publication reviewed by two or more experts of observations and experiments conducted by scientific researchers, may be disproven tomorrow. Take the idea that the sun is the centre of our solar system. Before 1514, geocentrism was the widely accepted view, in which bodies in our solar system orbited around the Earth. There were even mathematical models, the Ptolemaic system, that could actually explain how this could be the case (and perhaps here is an example of when mathematics suited an incorrect theory). It wasn’t until Nicolaus Copernicus presented a new model, and later Johannes Kepler and Galileo Galilei provided new observations to support this novel way of thinking, that paved the way for heliocentrism and a simpler mathematical model. Occam’s razor wins again.

Am I telling you not to believe what reporters say on the news? Kind of, yes. Am I telling you not to take as fact what scientists publish as scientific literature? Kind of, yes. Am I telling you not to trust anything that the scientific community puts forth? Absolutely not. On the contrary, I’m suggesting you think for yourself. Educate yourself in as much of the basic fundamentals of the topic as you can and decide whether to agree or disagree with their conclusions.

What I’m trying to advise is to become scientifically literate. Through searching, reading and analyzing scientific literature, I advise you to understand what researchers did, what results they obtained and how they interpreted these results. Another important factor is why researchers were interested in working towards their discoveries: what is the motivation for their work? And for my science pals, I didn’t forget about you. By being aware of the structural format, could you write in a way that captivates fellow peers and others to read and easily comprehend your work?

This is what this episode will aim to achieve. I will discuss, while introducing as little bias as possible, what I think about the most important aspects of finding, reading, analyzing and writing scientific literature, in a way that makes everyone think critically about the science and determine whether the minimally biased conclusions can be deemed, at the very most, “good enough to be fact.”

There’s a lot to discuss about scientific literature. So let’s get to it.

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Most of this information was obtained from many articles and videos discussing the topic of scientific literature, from experts encompassing all scientific fields. All sources will be mentioned in the description.

My goal is to somehow increase our level of scientific literacy by discussing the ins and outs of scientific literature. Whether you are at a baseline level, whether you’ve taken science courses in school, whether you are a science enthusiast, or whether you are working in a scientific discipline, there are likely some useful tips in this episode that will benefit you in some way. Science is simple at its core, however its when we utilize fundamental knowledge to expand our understanding of the real world through experimentation, or apply policies and procedures based on the interpretations of experimental results, that things start to become complicated. It is the skill of scientific literacy that will keep all individuals grounded in rationalism.

As I’ve stated, the average person obtains the breakthroughs in science via news shows, articles, or some broadcasting media. Hell, perhaps you also get it from social media as well, shared or retweeted by a close relative or respected friend. In fact, a recent CNN poll found that an astonishing 75% of Americans get their news from emails or social media updates. Normally, these are not examples of scientific literature, but summaries or paraphrasing descriptions. How do you find real scientific literature?

Within these news articles, authors or broadcast hosts often reference or cite the information they are addressing. In written media, these may come in the form of a bibliography at the end of the article, or a hyperlink which you can click that redirects your page to the source of their statement. Video and audio media is a bit more, convoluted. For example, as listeners of this podcast, how many of you actually look at the references I have on my website, addressing articles on specific expressions, or sources of my scientific topics? I would honestly guess no one. No one truly has the time and convenience to check, especially if they’re not extremely invested in the topic. How about the citations listed under YouTube videos from SciShow, Smarter Every Day, or ASAP Science? Do you really look at whether what they say is true? Or do you unconsciously perform the well known fallacy known as argument from authority, taking what a seemingly credible person on the topic reports? Is there even an expression that involves “an elephant in the room”??!

For the sake of argument, consider this CBC quote from May 19th this year: “Dr. James McGill from the University of British Columbia’s latest clinical trial stated that Canadian COVID-19 patients are often women aged 25-50.” This is not a particularly devious quote. I mean, it could be true. Perhaps you can check if COVID-19 patients are actually women aged 25-50. Perhaps you could also check if there is a Canadian clinical trial happening at the University of British Columbia. Perhaps you would be pleasantly surprised to know that there was no CBC report, and that the name James McGill comes from a show I’ve been binge watching during this pandemic… Anyone could say anything, you just need to check the information yourself, even if it seems credible.

Nonetheless, we start with these sources. The point is to start somewhere, if you can. Have you ever been told that Wikipedia is not a great reference for obtaining knowledge? That’s a load of nonsense. Yes, of course it’s feasible for anyone to modify Wikipedia pages. Except that’s not even true. As a test, I created a Wikipedia account to see if I could modify the pages of important relevance, like the pages for SARS-CoV-2, or global warming, or vaccines, and I am not able to due to a protection feature. However, even without an account, one could look at the sources for specific statements on, say, global warming, at the bottom of its page. These often reference scientific literature which you can browse. The subscription-base or open-source nature of these articles will be explained in a future episode.

You can get scientific literature simply by using any search engine as well. If you’re trying to get an overview on a specific topic, I would suggest searching something like: review about, and then fill in the blank. You want a scientific overview of SARS-CoV-2? Boom, type that format in your Google search and the the second and fourth link as of May 26th are true examples of scientific literature. These articles will be mentioned in the description. Now remember, that although these are published in scientific journals, they are reviews that discuss other scientific papers that introduce some novel concepts into their fields. It is important to read these reviews to get the overall big picture of the topic, and if still interested in knowing further, proceed to get the original sources that they talk about.

I said second and fourth link because these articles are in credible scientific journals. How can you limit your search results to just finding these? You can use specific search engines, like Scopus or Web of Science, which will also be linked in the description. However, these search engines are paid-for services, and I’m going to guess that most of you aren’t university library personnel. Google provides the Google Scholar service that looks specifically for scientific literature and even lists how many times the article has been cited, often a metric that determines its importance to the topic in question. Another one is PubMed, which is a database that contains 30 million citations and abstracts on biomedical literature. In my field of biological sciences, this is my first stop in learning more about a particular topic, and often has filters that permit more recent research, or specific authors. I won’t go into the tips and tricks of database searching, like using the PICO framework, Boolean operators, wildcards, fieldtags, and the like, (though sources for optimizing your search will be listed in the description), but utilizing these databases can help address your craving for scientific literature collection, just like going to Dairy Queen can help address your craving for soft-serve ice cream.

So you’ve collected some scientific literature and you’ve looked at whether its source is credible. What I mean by that is you saw where it is published and looked at whether this was a credible location for scientific discussion. What’s next?

Time to read it, right? Not quite yet. You’ve collected a vast array of scientific literature in your initial search, perhaps 5-10 scientific papers of a topic of interest, if even possible, each anywhere from 10-20 pages in length. Adjusting for the fact that the text is often divided into two columns per page, at a relatively small font, no figures, let’s say 750 words per page. My rough estimate, considering all these factors, as well as the average reading speed of 250 words per minute, and the complicated nature of the text, a real read through per paper would be around 45 minutes to an hour. That’s at the very least 5-10 hours of reading. No one will do that, no one will want to that, even people paid to do this for a living are not going to do that.

This leads me into the structure of most scientific literature. Now I’m excluding patents and reviews. And if you recall from just a moment ago, what I want to talk about now are the sources that are referenced in scientific reviews of a grander topic. Now, scientific papers have a format that has lasted for hundreds of years. It was only in the early 19th century that the idea of publishing papers in a catalogue was introduced, by an English mathematician and engineer named Charles Babbage (https://www.enago.com/academy/a-brief-history-of-the-catalogue-of-scientific-papers/) (https://www-nature-com.proxy.bib.uottawa.ca/news/the-catalogue-that-made-metrics-and-changed-science-1.22961). The format of the paper can be juxtaposed with the format for any story: 1) abstract: almost like the synopsis at the back of a book, only with spoilers. It contains brief mentions of the other sections of the paper, and provides you with a general idea of whether this paper is something you want to fully read; 2) Introduction and the Materials & Methods: or the exposition of a story. Why are researchers interested in this topic, what sort of knowledge should the reader know before learning about what they did, and how did they conduct their experiments; 3) Results: these are the rising actions of the a story. Experiments that build upon themselves to paint a picture for the reader; 4) Discussion; I would compare this to the climax and falling action portions of a story. Each experiment led to some results that can be interpreted in a number of ways. Authors will likely choose one way and explain their reasoning for why its not the others. Think of it like having multiple climaxes, an urban legend right? Anyway, this section would also include limitations to their study, and where they think the future directions are for their work; lastly 5) Conclusion; the resolution of their story, ground their work via the significance of it all and explain how their work has advanced knowledge in their scientific field.

All papers follow this format and depending on your purpose for obtaining the paper and how much time you want to invest in it, you can pick and read only certain sections. For general science lovers, I would recommend reading a paper from the beginning. However, despite my juxtaposition, papers are usually never read as a story from start to finish. Dr. Pete Carr, from the University of Minnesota, has a few key suggestions for anyone before they invest a chunk of their time into a scientific paper. 1) Read the title and keywords, these will often tell you whether the scope of the paper is general enough for your understanding, or very specific and requires more fundamental knowledge. 2) Read the abstract, the synopsis of the paper, which usually is only at most 5 minutes of your time. 3) Read the conclusions. That’s right, jump to the major spoilers of the story and find out whether their conclusions are relevant to your quest for knowledge. From here, you can jump into the intro, results or discussion section, depending on what you want to know more about.

Now let’s say you’re a keener and went through the paper already. Congratulations, you’ve done something that a majority of people have not done in its entirety. Now, did you understand the paper? Did you take notes as you read the paper, highlight terms or concepts that didn’t make a lot of sense? Do we just take what the authors say as truth, or with a grain of salt? (I HAVE to put expressions somewhere)

Understanding a paper is quite honestly extremely difficult, even for a graduate student, even for a professor, even for an expert in the field. For myself, I often have to read a paper 2-3 times in order to fully grasp what the authors are trying to show me. And that’s not an uncommon opinion. In an article written in the Conversation by Dr. Gordon Rugg from Keele University, he states that academic writing is deliberately written in boring, unemotional prose. Why? One example he cites was the popularity of a pseudoscience called Mesmerism. In the late 1700s, an intellectual named Franz Anton Mesmer “believed that illnesses were caused by blockages that interfered with the healthy flow of magnetic fluid through the body”. He proceeded to magnetize trees in a park and have people with ailments hug or interact with these magnetized trees. His manipulative language fooled even those of highest societal esteem. Dr. Rugg states other reasons, like limited word counts, or precise technical terms special to a field, which are “inevitably a burden to learn for the first time”.

Therefore a lot of the peer review process, which I will discuss more in detail later, is focused on the methodology and results, including the statistical tests and author interpretations. These are the most important things about a scientific paper, and the most heavily criticized. As a general reader, your goal is to align each experiment with each result. Is a double-blind randomized clinical trial the best approach? What is a double-blind randomized clinical trial? What I am saying is, you don’t need to know the detailed description of how to do one, but a simple secondary search on whether a double-blind randomized clinical trial is a method that is commonly used to assess the effectiveness of a treatment to a disease would be sufficient. Knowing whether the method they used is a valid way of determining the truth, is probably the most important thing a general reader should understand.

The statistics, unfortunately, or a different matter. For a general reader, I acknowledge that the numerical statistics you can find in scientific papers that describe the significance of their findings are inherently complex, like looking at the digital interface of the Matrix. These are better described in reviews or summaries of mainstream journal articles to which you can at least trace their statement to somewhere in the paper. Statistics, in its enormity, will have to be covered in a future episode.

To my science pals, I haven’t forgotten about you. Surely you have once looked at a blank screen with the blinking text cursor waiting for the right words to come for your thesis or paper writing. I would imagine you also look at commonly cited works in your field, hoping to articulate your work with similar vocabulary and prose. Perhaps, to the horror of the average reader and in the words of Dr. Daniel Oppenheimer, “[ignore the] consequences of erudite vernacular utilized irrespective of necessity, [or the] problems with using long words needlessly”. Dr. Oppenheimer is the winner of the Ig Nobel Prize, an honour given to to research that makes people laugh, then think. For example, the 2019 Ig Nobel Prize in physics was given to a team of researchers studying how and why wombats make cube-shaped poop (http://meetings.aps.org/Meeting/DFD18/Session/E19.1). However, most scientific writing makes people think, hard, so hard that their head aches, then quit.

I will have a whole episode on scientific writing, so I won’t stress most of the research on it here. There are many sources that provide extremely detailed notes on how to write science elegantly. The main point that researchers often forget is that your thesis, your paper, is a story. It’s not a journal entry, not a pit of unlinked ideas, but a narrative journey through your work. In a feature article in one of the most prestigious scientific journals of our time, Nature, six experts from various scientific fields working around the world summarize the top 6 goals of writing a first-class paper: 1) Keep a clear message; what is the main point you want your reader to grasp despite not understanding anything else, 2) Maintain a framework; if you write a certain way, continue writing that way. For example, if you construct each paragraph as a content-context-conclusion sandwich, have every paragraph written that way, 3) Be confident in your case; sure you will have limitations to your work, but what did you do to address them, or why is your methodology better than others, 4) stop using boring generic nouns; these are littered in scientific writing, adding suffixes like -ance, -ment, -ation to satisfying verbs. Affirming an idea becomes the affirmation of an idea. 5) stay simple but interesting; did participants read assertions whose veracity was either affirmed or denied by the subsequent presentation of an assessment word? Or did participants read sentences that were followed by the words true or false?; and lastly 6) widen your audience; why only write to your peers when you can write to the next generation of scientists or the proportion of the general public trying to be scientifically literate?. When not done properly, scientific writing often traverses to the language Dr. Steven Pinker coined as “academese”. Try to avoid this transition as best as you can.

That brings us to the last segment of scientific literature. You will often hear that scientific literature undergoes what is called a peer review, and this distinguishes it from the anecdotal knowledge of our past predecessors. So to further define scientific literature, I’d like to briefly go over what peer review essentially means.

There are over 12,000 journals listed in the ISI Web of Science and these capture 95% of all scholarly citations. I should mention that each journal has their own process of peer review, but in general each process is fundamentally similar. As stated in A Guide to Peer Review in Ecology and Evolution by the British Ecological Society, peer review improves the quality of articles that are published, provides an assessment of the science in the literature, assists the editorial decision making process and acts as a gatekeeper for unethical practice. Throughout their career, academics volunteer to peer review papers, as part of their dedication to their field. VOLUNTEER. These reviews often remain anonymous, on the authors end (single-blind), or also on the reviewer’s end (double-blind). There are also open peer review processes that allow the identity of both parties to be known. In a general sense, the workflow of peer review can be summarized as follows: Author sends in a manuscript to a journal’s editorial office for a basic suitability check, where administrators send it to the editor who determines whether it fits within the scope of the journal, who sends it to an associate editor with more specific expertise for a basic methodology and results check, who sends it to at least 2 reviewers with even more specific expertise for a thorough read through of the manuscript in its entirety, who sends it back to the associate editor for them to review their comments and create an evaluation report for the editor who reviews the report and ultimately makes the final decision which is presented back to the original authors. WOOF. Therefore, this one manuscript is read at the very least, 4 times by experts in the field. Altogether, in most journals of high acclaim, this process allows for less than 20% of submitted manuscripts (the rough unformatted papers) to be accepted for publication.

The importance of this process is emphasized at the reviewers stage. Elaborated in a lecture by Dr. Richard Pearson at UCL, reviewers will seek to answer 4 questions: 1) are the data appropriate?; 2) have the analyses been run correctly?; 3) do the conclusions follow from the results?; and 4) is the work placed in the context of previous studies?. This critique allows for only the most sound science to pass through. Think of it as being a teacher, and having homework assigned to you, that will be graded by another teacher. Of course, the answers to the problems researchers face are not as simple as knowing that 2 is the answer to 1+1 (though the mathematical proof to this is actually complicated). The solutions to today’s scientific questions require debate, and need the inclusion of opinions from many experts to determine what is true.

And that will cover it. I acknowledge there is much of the aspects of scientific literature that I may have left out due to time, and realize I will have much content to discuss in future episodes of this podcast. What I’ve briefly covered are the 5 aspects that I believe summarize the main ideas behind scientific literature, and can be reiterated by the following: 1) searching, 2) reading, 3) understanding, 4) writing and 5) reviewing. If you’re into acronyms, just gotta remember SRUWR.

By understanding each aspect, we can easily see the significance of scientific literature and respect researchers who are striving to get to the truth. Optimizing the authors and the readers experiences at each step is crucial to better communication that describes the nature of reality.

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For this episode, I would again like to “walk the walk”, using the information from the previous section to present to you an idea of my own. I have designed an article that describes the importance of the work I’ve been doing for the last 2 and a half years of my life. Due to copyright issues with the university, I will not be presenting the extensively detailed data I’ve obtained and published in my MSc thesis (though you can check it out in 6 months from now once the embargo on it is lifted). But what I have attempted to do was write about my work in an interactive, easy to read format that both my peers and the general public can relate to. This piece of writing, is a format in which I hope all research papers are complemented with in the hope of including everyone to embrace your work, and evidently, share your love of science with the world at large. You can find it on my website at kjbmercurio.com/masters. That’s kjbmercurio.com/masters. There’s a comment section at the bottom of the page, so please if you read it let me know what you think, what areas that you liked, or disliked, the most.

That does it for season 1! Thanks for listening to this special season finale of… Metaphorigins. Remember to rate and subscribe for more episodes and to follow the podcast on Instagram for updates on the season 2 return coming to you sometime in July. But until then, stay skeptical but curious.
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