Category Archives: Blogging

How to read (and perhaps even write) a scientific paper


This post was inspired by this other one, featured in WordPress’ Freshly Pressed section, on how should non-scientist read a scientific paper.  While the approach presented therein is both valid and valuable, I’d like to address the way I think a scientist should read a paper, given the fact that we need to read a lot of them at all times. Each scientist has their own reading style, not to mention their own writing style, and while my CV could indicate I don’t know how to do neither one, here I present to you my scientific-paper-reading style which I consider to be the most suitable for me.

I’d like to start by emphasizing that I dive into scientific literature in a bona fide fashion. That is not to say I’m totally naive or even gullible, but even when science is all about questioning and casting doubt onto all sorts of claims, we can’t re-develop every bit of science we need. At a certain point we must start *gasp* believing trusting other scientists’ claims. Reading in what I call bona fide is not mutually exclusive with critical reading. This sort of scientific trust is earned, to a degree, mostly by two indicators: Author’s preceding reputation at the time of publication of any given paper as well as the journal’s. Both indicators aren’t without controversy and flaw.

The way I read a paper is the following: I start with the Abstract, then follow with the Conclusions, then the Results section, sometimes I read the details of the methodology and seldom read the Introduction. Let me explain.

I read the abstract first because I read in bona fide as I hope the authors wrote the paper in bona fide. If properly written, the abstract should include all the relevant information as to what was done, why, and how but also point to the knowledge derived from it all: Their conclusions! and that is why I follow with that section. I’m interested in knowing what the authors learned and ultimately want me to learn about their study. Once again I’m reading in bona fide, so I hope they weren’t tempering their results to fit their preconceptions, that all experiments were thoroughly self-judged, validated, correlated, referenced and controlled. Recently, my sister Janet, who is a physicist working on her PhD in neuroscience, told me about some friends of hers who never (shall I say, never have I ever?) read the conclusions as to not becoming biased by the authors. To me it seems like too much work having to scrutinize every piece of data again in order to come up with my own conclusions when authors, collaborators, people on the hallway down the lab (optional), referees and editors (vide infra) have already (hopefully) done it (properly). Still I put on my scientist badge and question everything I critically read in the results section trying thus to understand how did the authors reached their conclusions and asking myself if I could come up with something entirely different. No? OK, how about something slightly different? Still no? Well, do I agree with the authors on their findings and their observed results? And so on. I like thinking that my critical reading process resembles the Self Consistent Field method which iteratively reaches the best wavefunction for a set of certain given conditions, but it never reaches the exact one.

The methodology section is a bit tricky, specially when it comes to computational chemistry. Back when I was a grad student, working in an inorganic chemistry lab, I’d only read the methodology if I had any plans of reproducing the experiment, other than that I didn’t care too much if reagents were purchased from Aldrich or Fluka or if the spectrophotometer was a Perkin Elmer one, I just expected authors to have purified their reagents prior to usage and calibrated all spectrophotometers. Now in computational chemistry I read about the methods employed, which functional and what basis set were used and why were they selected are my most frequent questions, but the level of theory is usually stated in the abstract. I also take a look at what methods were used to calculate which properties; these questions are important when we have to validate our trust in the results in front of us.

Finally, I seldom read the introduction because, if the paper is relevant to my own research, I don’t need to read why is important or interesting, I’m already sold on that premise! that is why I’m reading the paper in the first place! If both me and the author act in bona fide, we both already know what the state of the art is, so lets move on because I have a ton of other papers to read. Hence, I read the introduction only when I’m trying to immerse myself in a new field or when reading something that seems interesting but which has little to do with my area of expertise. There is another reason why I almost never read introductions and that is that, even when I try to work in bona fide, there are a lot of people out there who don’t. Twice have I received the reviews from a mysterious referee who believes it would serve the work a great deal to cite two, maybe three, other papers which he or she lists for your convenience, only to find out that they all belong to the same author in each case and that they are not quite entirely related to the manuscript.

In the title of this post I also try to address the writing of a scientific paper, although I’m not an authority on it, I think today’s key phrase is bona fide. So to young and not so young scientists out there I’d ask you to write in bona fide, please. Be concise. Be convincing. Be thorough and be critical. This is science we are doing, not stamp collecting. It shouldn’t be about getting all sorts of things out there, it is about expanding the knowledge of the human race one paper at a time. But we are humans; therefore we are flawed. More and more cases of scientific misconduct are found throughout the literature and nowadays, with the speed of blogging and tweeting, we can point at too many of them. The role of bloggers in pointing this frauds, of which I’ve written before here, is the subject of recent controversy and possibly the topic of a future post. We are all being scrutinized in our work but that shouldn’t be an excuse to make up data, tinker or temper with it, to push our own personal agendas or to gain prestige in an otherwise wild academic environment.

I for one may never publish in Science or Nature; I may never be selected for any important prize, but even the promise of achieving any of those is not worth the guilt trip of lying to an entire academic society. I try then, to always remember that science is not about getting the best answers, but about posing the right questions.

What is your own style for reading papers? Any criticism to my style? How different is the style of a grad student from that of a researcher?

As usual thanks for reading, rating and commenting!

Summer internships are Over


For the last five weeks we had guests in our lab coming from different places of the country: Tepic (west), León (Center) and Mexico City (Right in the middle!). During those five weeks they worked in the field of computational chemistry helping our research efforts with a couple of drug carrying molecules. They learned about computational chemistry and drug design; about wavefunctions and density functionals; about population analysis and vibrational frequency analysis. Dead hours were a bit complicated to handle because the convergence of each calculation takes some time and, as opposed to a wet-chemistry lab, I couldn’t just ask them to purify starting materials or distillate solvents. A question to other theoretical/computational chemists: What could I have asked young undergrad students (with backgrounds ranging from engineering to pharmacy) to do during those dead hours? What did I do wrong? Anyway, they manage to spend a good time since they all got along quite well.

Now they are back to their hometowns getting ready for the congress, hosted by the same organization that awarded them the stipend to come and spend their summer with us (The Dolphin Program / Programa Delfín) as well as to going back to school in a few more weeks. I asked* them to write a guest post for the blog telling their experience, which is presented below. Thanks to you all for choosing our lab to get your internship this summer!

Javier Camacho (Mexico City)

Javier_Delfin_2013Hi, I’m Javier from ESIQIE-IPN
The dolphin program has given me the opportunity to experience how is to be in a high-level scientific research. Login to CCIQS next to the imminent Dr. Joaquin Barroso Flores, left me a pleasant experience. The great contribution that gives this line of research has allowed me to meet new horizons, beyond the area of engineering, to which I belong.
The theoretical chemistry and computational chemistry together, are a great weapon to develop virtual optimizations that allow us to find drug transport agents, without making the vast amount of laboratory tests that are required. Explaining that this is one of the many applications that can be used.
To undertake this experience has left me very satisfied, be guiding a person who likes his work and want to show what he knows, it makes me very happy. After these long weeks of work and perseverance, with certainty affirm the interesting and productive it is to be part of the investigation in Mexico.
I thank the Dolphin Program, gives CCIQS the UAEM-UNAM and Dr. Joaquin for opening the doors to this great opportunity to start my story as a researcher.

 

Paulina Pintado (Tepic, Nayarit)

la fotoHi my name’s Paulina and I came as part of Dolphin Research Program that gives the opportunity of participates in a real work of investigation with a professional at the topic. In this occasion I came to work with Ph.D. Joaquin Barroso in a small project of his line of research; namely theoretical drug carriers design. In this six weeks besides to learn more aspects about my career, in this case Theoretical Chemistry applied to pharmaceutical industry; I tested the experience of travel to another town just by myself, live with people from different parts of the country with distinct customs and visit few places of the town.
This summer will always be memorable ‘cause this internship is an important event for my professional experience and also for my personal development and I hope many others students have the courage to try get into the world of scientific research.
So just remains for me to thank to Ph.D. Joaquin Barroso for giving me the chance to do this internship in his lab I hope you continue having success in your work, I feel pretty glad to met him and my others research’s mates.

 

 

Daniel Carteño (Mexico City)

Ey my name’s  Daniel and this summer of  2013  i had been the opportunity to do a research  internship in Toluca under P.H.D. Joaquin Barroso, and during this period of time I´ve learnt a bit about His research work, not only this is  an important experience for my educational history, but it also is for my personal life. Learnt about theoretical chemistry open my vision of this discipline, because when I thought about chemistry I´ve never imagine a computational laboratory, this the most important part, nowadays the researches have been removed due to  they are so expensive and finally the conclusion  is not expected, when you use a super computer like me and my work team used, it doesn’t matter if you have a mistake  or do something wrong, only you have to write again the keywords and the only thing you spend is time. Even in Mexico theoretical chemistry is not famous in my opinion is a useful work tool. This research internship was highly satisfactory and hope do it again i´m glad

*Their contributions were completely voluntary and no editing of their original texts has been made.

Summer Internships


This week has been a happy one since four new additions to our staff have been made, at least for the summer, that is. Paulina, Eliana, Javier and Daniel have come to our lab from various different towns across the nation to spend six weeks working hard in small projects related to our lines of research; namely theoretical drug carriers design. This time the drug under study is known as GTP or 3-phenyl(1H-[1]benzofuro[3,2]pyrazole and calixarenes will once again act as the potential carriers.

20130626-122705.jpg

Left to Right: Daniel, Javier, Paulina and Eliana
(Summer Interns – 2013)

They all came as part of the Dolphin Research Summer Program (link in Spanish only) in which college students spend a few weeks doing research in the lab of their choosing. This is the first time I participate as a tutor and I find it a great opportunity for young students to get familiar with certain aspects of science they wont learn inside school.

So far these past three days have been quite intense with them learning how to edit and submit a Gaussian calculation in a Linux environment. I’ve already taught them about geometry optimizations, frequency analysis, (natural) population analysis and Fukui reactivity indices calculation. There is much more to learn still, of course, but so far so good. I believe the major drawback so far has been their own eagerness since they’d like to have all the data imediately! Unfortunately they’ll have to wait for their initial calculations to converge. We started this week by doing some simple analysis of all the properties described above for the Cytosine-Guanine base pair at the B97D/6-31+G(d,p) level of theory. Luckily their calculation crashed promptly, and I find that lucky because that gave me the opportunity to teach them how to relaunch a failed calculation, which, unfortunatelly will happen more often than not.

So, welcome guys! Thanks for choosing this lab for doing your internships. I hope you find our research interesting and motivating, may this be the first step into a full time research career. Also, kudos to the Dolphin Staff for helping promote science in young Mexican students. Stay tuned for a guest post from all of them once they finish their time here.

RealTimeChem week 2013 #RealTimeChem


RealTimeChem, in its first week-long edition, is coming to your Twitter feed next Monday April 22nd 2013, and I for one intend to participate.

I look forward to this event in order to get in touch with other chemists, not only theoretical but experimental ones as well, around the world sharing a passion for chemistry and technology. I guess most of the participants will be experimental chemists who will amaze us with their videos and pictures of cool looking reactions; I hope we, here at our computational lab, are up to the challenge with our calculations.

Participating is really simple, just Tweet as little or as much as you want to share about your work or studies around chemistry under the #RealTimeChem hastag and follow @RealTimeChem. There is also a group and an event set up on Facebook, check those out too. As I write this, its Friday at 8:oo PM and I’m still in the office, which means I have a lot of work to do, therefore I don’t feel like writing about all the details of the event, specially when others have done so in a much more eloquently fashion: Check out these posts (as well as the entire content of their blogs, they’re very cool!) by Dr. Galactic and The Organic Solution for all the details about the event’s mechanics and, yes, even prizes to the best tweets.

So get on board and tweet all week long under the #RealTimeChem hashtag  and share your work with the world the way no journal will ever do: in real time and with the uttermost embarrassing methodology honesty.

100,000 visitors!


This morning at around 9 AM, I guess, this little blog of mine reached a significant milestone: It reached 100,000 visitors!

The blog started about 3.5 years ago when I was still living in Romania working at the lab of the late Prof. Dr. Ioan Silaghi-Dumitrescu. Back then I started the blog as a way to make my research visible to others and maybe in that way I could gain some notoriety which could help me in the near future to land a fine research position. None of that happened. I remember we were having some issues with some PCM calculations in the lab and after a lot of hard work and a lot of asking we gather some tips to work with implicit solvation models in Gaussian. Prof. Silaghi suggested we should write them down and put them on the wall of the lab so we had them available at all times; it was then when I suggested we could place them in my little blog so we had them available online. This happened in September 2009, three years ago, and little did I know, this post became quite popular, it is still one of the most visited ones in the blog. Later on we had a similar problem while trying to visualize Natural Bond Orbitals, there was too much information but it was all scattered, so we did it again, we gathered some of the info and made a new post which became also quite popular.

100,012 visitors this morning. Thanks!

Little have I written about my own work, mostly because of fear of being scooped, I guess.

I’d like to thank every reader who has ever liked, commented, rated, favorited, shared, reblogged, blogrolled, recommended any of my posts and the nearly 200 people who have subscribed or followed this little blog, as I like to call it.


This is the first time I reblog a post from a fellow computational chemist and the reason why I do it is because of its beautiful simplicity and usefulness. Given the scope this blog has taken I think this post becomes most appropriate. This post will show you how to create an energy level diagram using nothing but MS Excel.
Kudos to ‘Eutactic’, from Australia, for coming up with a nice solution to this problem. Check out his blog at eutactic.wordpress.com.
Thanks for letting me repost it 🙂

eutactic

I worked out a very quick and easy way to generate level schemes in Excel, based on a query from one of the other students in the group. Normally I would resort to something like the astonishing TikZ for this sort of task, however our group is very much a Microsoft Office ‘What You See Is A Metaphor For Cosmic Horror‘ group and recommending that a colleague learns two new markup languages to produce a figure is probably not helpful in the short term. One of the issues with charting energy levels in Excel is that levels are typically represented by horizontal bars connected at their vertices with lines representing transitions. Whilst Excel does have a horizontal bar as a marker, it possesses two show-stopping limitations:

  1. It is only uniformly scalable, and can only be scaled so far – we cannot make it anywhere near wide and…

View original post 222 more words

Stop SOPA


As a scientist I believe the free share of information (which is not the same as to say of property) should prevail throughout the vastness of this global tool we have available. I’ve worked for private companies and I do believe in their right to keeping private the information they have invested in. But with SOPA there is an issue with freedom of speech and nobody wants to have their accounts monitored by a government, any government. Please read “1984” by George Orwell to have a better understanding of how false security and safety is not worthy of a captive society under surveillance.

You have all gained something by the free share of knowledge in this blog, as I’ve had from other online resources such as the CCL. If SOPA is passed, then I, we, may not be able to provide help with the use of commercial software such as Gaussian, for instance, and the progress of science would be directly hurt.

I do not endorse piracy. Private companies are entitled to profit as a return of their investments. But laws such as SOPA would only hurt those trying to make the most out of the largest communication media ever created in the history of mankind, while doing little to protect investors and developers. Many are the examples of developments arising from public effort: Wikipedia; Linux; OpenGL; The GNUproject. Open share of ideas have brought this and many other resources which ultimately result in the development of science and technology. Please read this article (in Spanish) by Dr. Alejandro Pisanty, a former teacher of mine at the Chemistry School. He was the head of the Academic Computing Services at UNAM, and one of the founders of the Computational Chemistry List (CCL); He most definitely knows a thing or two about information technologies.

It should be clear that the openness of the Internet has clear advantages as seen a year ago when the people from Tunisia got organized online and got rid of a dictatorship. Control of communication is a common treat of fascist and authoritative regimes. Information set them free.

Please rate/like/comment this post if you are also against SOPA and for the freedom

of speech over the Internet.

http://sopastrike.com/strike/

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