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Papers for the 21st Century


The format of a research paper hasn’t changed much throughout history, despite the enormous changes in platforms available for their consumption and the near extinction of the library issue. Convenient electronic files such as PDFs still resemble printed-and-bound-in-issues papers in their layout instead of exploiting the seemingly endless capabilities of the electronic format.

For instance, why do we still need to have page numbers? a DOI is a full, traceable and unique identification for each work and there are so many nowadays that publishers have to pour them out as e-first, ASAPs, and just accepted before having them assigned page numbers, a process which is still a concern for some researchers (and even for some of the organizations funding them or evaluating their performance). Numbers for Issues, Volumes and Pages are library indexes needed to sort and retrieve information from physical journals but in the e-realm where one can browse all issues online, perform a search and download the results these indexes are hardly of any use, only the year is helpful in establishing a chronological order to the development of ideas. This brings me to the next issue (no pun intended): If bound-issues are no longer a thing then neither should be covers. Being selected for a cover is a huge honor, it means the editorial staff think your work stands out from the published works in the same period; but nowadays is an honor that comes to a price, sometimes a high price. With the existence of covers, back-covers, inner-covers and inner-back-covers and whatnot at USD$1,500 a piece, the honor gets a bit diluted. Advertisers know this and now they place their ads as banners, pop-ups and other online digital formats instead of -to some extent- paying for placing ads in the pages of the journals.

I recently posted a quick informal poll on Twitter about the scientific reading habits of chemists and I confirmed what I expected: only one in five still prefers to mostly read papers on actual paper*, the rest rely on an electronic version such as HTML full text or the most popular PDF on a suitable reader.

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What came as a surprise for me was that in the follow up poll, Reference Manager programs such as Mendeley, Zotero, EndNote or ReadCube are only preferred by 15% while 80% prefer the PDF reader (I’m guessing Acrobat Reader might be the most popular.) A minority seems to prefer the HTML full text version, which I think is the richest but hardly customizable for note taking, sharing, or, uhm hoarding.

https://platform.twitter.com/widgets.js

I’m a Mendeley user because I like the integration between users, its portability between platforms and the synchronization features but if I were to move to another reference manager software it would be ReadCube. I like taking notes, highlighting text, and adding summaries and ideas onto the file but above all I like the fact that I can conduct searches in the myriad of PDF files I’ve acumulated over the years. During my PhD studies I had piles of (physical) paper and folders with PDF files that sometimes were easier to print than to sort and organize (I even had a spreadsheet with the literature read-a nightmarish project in itself!)

So, here is my wish list for what I want e-papers in the 21st century to do. Some features are somewhat available in some journals and some can be achieved within the PDF itself others would require a new format or a new platform to be carried out. Please comment what other features would you like to have in papers.

  • Say goodbye to the two columns format. I’m zooming to a single column anyway.
  • Pop-up charts/plots/schemes/figures. Let me take a look at any graphical object by hovering (or 3D touching in iOS, whatever) on the “see Figure X” legend instead of having to move back and forth to check it, specially when the legend is “see figure SX” and I have to go to the Supporting Information file/section.
  • Pop-up References. Currently some PDFs let you jump to the References section when you click on one but you can’t jump back but scroll and find the point where you left.
  • Interactive objects. Structures, whether from X-ray diffraction experiments or calculations could be deposited as raw coordinates files for people to play with and most importantly to download** and work with. This would increase the hosting journals need to devote to each work so I’m not holding my breath.
  • Audio output. This one should be trickier, but far most helpful. I commute long hours so having papers being read out loud would be a huge time-saver, but it has to be smart. Currently I make Siri read papers by opening them in the Mendeley app, then “select all“, “voice“, but when it hits a formula, or a set of equations the flow is lost (instead of reading water as ‘H-Two-O‘, it reads ‘H-subscript Two-O‘; try having the formula of a perovskite be read)
  • A compiler that outputs the ‘traditional version‘ for printing. Sure, why not.

I realize this post may come out as shallow in view of the Plan-S or FAIR initiatives, sorry for that but comfort is not incompatible with accessibility.

What other features do you think research papers should have by now?



* It is true that our attention -and more importantly- our retention of information is not the same when we read on paper than on a screen. Recently there was an interview on this matter on Science Friday.
** I absolutely hate having a Supporting Information section with long PDF lists of coordinates to copy-paste and fix into a new input file. OpenBabel, people!

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I’m done with Computational Studies


I’ve lately reviewed a ton of papers whose titles begin with some version of “Computational studies of…“, “Theoretical studies of…” or even more subtly just subtitled “A theoretical/computational study” and even when I gotta confess this is probably something I’ve done once or twice myself, it got me thinking about the place and role of computational chemistry within chemistry itself.

As opposed to physicists, chemists are pressed to defend a utilitarian view of their work and possibly because of that view some computational chemists sometimes lose sight of their real contribution to a study, which is far from just performing a routine electronic structure calculation. I personally don’t like it when an experimental colleague comes asking for ‘some calculations’ without a clear question to be answered by them; Computational Chemistry is not an auxiliary science but a branch of physical chemistry in its own right, one that provides all the insight experiments -chemical or physical- sometimes cannot.

I’m no authority on authoring research papers but I encourage my students to think about the titles of their manuscripts in terms of what the manuscript most heavily relies on; whether it’s the phenomenon, the methodology or the object of the study, that should be further stressed on the title. Papers titled “Computational studies of…” usually are followed by ‘the object of study’ possibly overlooking the phenomenon observed throughout such studies. It is therefore a disservice to the science contained within the manuscript, just like experimental papers gain little from titles such as “Synthesis and Characterization of…“. It all comes down to finding a suitable narrative for our work, something that I constantly remind my students. It’s not about losing rigor or finding a way to oversell our results but instead to actually drive a point home. What did you do why and how. Anna Clemens, a professional scientific writer has a fantastic post on her blog about it and does it far better than I ever could. Also, when ranting on Twitter, the book Houston, we have a narrative was recommended to me, I will surely put it my to-read list.

While I’m on the topic of narratives in science, I’m sure Dr. Stuart Cantrill from Nature Chemistry wouldn’t mind if I share with you his deconstruction of an abstract. Let’s play a game and give this abstract a title in the comments section based on the information vested in it.DcJCrr_W0AQCNQZ

DFT Textbook in Spanish by Dr. José Cerón-Carrasco


Today’s science is published mostly in English, which means that non-English speakers must first tackle the language barrier before sharing their scientific ideas and results with the community; this blog is a proof that non-native-English speakers such as myself cannot outreach a large audience in another language.

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For young scientists learning English is a must nowadays but it shouldn’t shy students away from learning science in their own native tongues. To that end, the noble effort by Dr. José Cerón-Carrasco from Universidad Católica San Antonio de Murcia, in Spain, of writing a DFT textbook in Spanish constitutes a remarkable resource for Spanish-speaking computational chemistry students because it is not only a clear and concise introduction to ab initio and DFT methods but because it was also self published and written directly in Spanish. His book “Introducción a los métodos DFT: Descifrando B3LYP sin morir en el intento” is now available in Amazon. Dr. Cerón-Carrasco was very kind to invite me to write a prologue for his book, I’m very thankful to him for this opportunity.

Así que para los estudiantes hispanoparlantes hay ahora un muy valioso recurso para aprender DFT sin morir en el intento gracias al esfuerzo y la mente del Dr. José Pedro Cerón Carrasco a quien le agradezco haberme compartido la primicia de su libro

¡Salud y olé!

The Gossip Approach to Scientific Writing


Communication of scientific findings is an essential skill for any scientist, yet it’s one of those things some students are reluctant to do partially because of the infamous blank page scare. Once they are confronted to writing their thesis or papers they make some common mistakes like for instance not thinking who their audience is or not adhering to the main points. One of the the highest form of communication, believe it or not, is gossip, because gossip goes straight to the point, is juicy (i.e. interesting) and seldom needs contextualization i.e. you deliver it just to the right audience (that’s why gossiping about friends to your relatives is almost never fun) and you do it at the right time (that’s the difference between gossips and anecdotes). Therefore, I tell my students to write as if they were gossiping; treat your research in a good narrative way, because a poor narrative can make your results be overlooked.

I’ve read too many theses in which conclusions are about how well the methods work, and unless your thesis has to do with developing a new method, that is a terrible mistake. Methods work well, that is why they are established methods.

Take the following example for a piece of gossip: Say you are in a committed monogamous relationship and you have the feeling your significant other is cheating on you. This is your hypothesis. This hypothesis is supported by their strange behavior, that would be the evidence supporting your hypothesis; but be careful because there could also be anecdotal evidence which isn’t significant to your own as in the spouse of a friend had this behavior when cheating ergo mine is cheating too. The use of anecdotal evidence to support a hypothesis should be avoided like the plague. Then, you need an experimental setup to prove, or even better disprove, your hypothesis. To that end you could hack into your better half’s email, have them followed either by yourself or a third party, confronting their friends, snooping their phone, just basically about anything that might give you some information. This is the core of your research: your data. But data is meaningless without a conclusion, some people think data should speak for itself and let each reader come up with their own conclusions so they don’t get biased by your own vision and while there is some truth to that, your data makes sense in a context that you helped develop so providing your own conclusions is needed or we aren’t scientists but stamp collectors.

This is when most students make a terrible mistake because here is where gossip skills come in handy: When asked by friends (peers) what was it that you found out, most students will try to convince them that they knew the best algorithms for hacking a phone or that they were super conspicuous when following their partners or even how important was the new method for installing a third party app on their phones to have a text message sent every time their phone when outside a certain area, and yeah, by the way, I found them in bed together. Ultimately their question is left unanswered and the true conclusion lies buried in a lengthy boring description of the work performed; remember, you performed all that work to reach an ultimate goal not just for the sake of performing it.

Writers say that every sentence in a book should either move the story forward or show character; in the same way, every section of your scientific written piece should help make the point of your research, keep the why and the what distinct from the how, and don’t be afraid about treating your research as the best piece of gossip you’ve had in years because if you are a science student it is.

 

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