Category Archives: Science
In the past I’ve avoided this topic for various reasons. First, because I strongly believe that focusing on labels perpetuates them, and as scientists, we should always rise above them, for is science and not scientists what’s important. I remember my former PhD advisor, Prof. Cogordan, saying that “Liberties are exercised, not demanded“. Take Rosa Parks, for instance, her refusal to move to the back of the bus was an exercise of her liberty, and one that moved to a profound change, alas not without turmoil. But should I really call it a label? since it applies to roughly half the potential brain power available in the planet it then becomes a relevant question. Are equality and political correctness mutually exclusive terms?
It could be argued that I talk from a privileged position being a male scientist but since I’m a Mexican, non-white, non-US-based, male scientist those privileges are only so many.
I first began drafting this post way back before November 2016, when the misogyny displayed by a presidential candidate was in everyone’s mind to such a large extent that even when it even seemed prone to cause his demise it didn’t. The women’s march in D.C. has proven the topic to be still quite relevant though, and next April 22nd, Earth Day, a scientists march will take place to protest against policies that put science -and therefore mankind- in jeopardy. Some particular issues associated with the march will be the communication gag orders against scientific federal agencies; the consequences of the travel-ban to scientists from black-listed countries and, of course, the threat of having a misogynistic environment on the status of women in STEM careers.
Fact: There is a clear selection bias since there is still a large number disparity between men and women in academia throughout the world and since the number of academic position is growing at a much lower rate than the number of scientists competing for such positions, the race has become tighter and usually women take the worst part of the deal. There is a leaking pipeline in which women don’t reach the end of the race. I imagine in some cases it may have to do with maternity as it is still conservatively perceived by most countries but issues like harassment and condescension are not to be ignored.
Fact: Scientific curiosity is innate to all human beings -which confirms the above mentioned bias- therefore talking about encouraging young women to pursuit a career in STEM is plain stupid; they don’t need to be encouraged they must stop being discouraged somewhere along the path. The playing field for both genders should be leveled or science risks loosing half the population in these dire times in which all the brain power available is much needed. Also, I fear the continuous talk about these disadvantages could be off-putting for future generations of women who might be interested in undertaking STEM careers. Leveling the field for female and male scientists should be done and not just demanded but details about the mechanisms to accomplish it are still unclear and vary from one institution to another. Here in Mexico, for instance, all public universities have collective contracts, therefore every scientist in a given level earns as much as another in the same level. In other countries salaries are personally negotiated and therefore each scientists earnings vary, which has led to women earning less on average. Now, the ease with which levels are climbed within an institution are also a matter for debate. Does this mean that earnings and positions are the main problems women face in academia? Could they be the best starting points? Is the rate of enrollment the root of the problem? If so, are us teachers and professors to blame?
Another reason why I avoided this topic was because it would seem so patronizing on my part to give a shout-out to women whose work in computational chemistry I so much admire when I myself could only aspire to one day have work of their quality. They definitely don’t need my praises because they have well earned all our admiration. Nonetheless, here is a link to a great directory of women working in computational chemistry in which some great names are found such as Anna Krylov, Gloria Tabacchi, Romelia Salomón, Patricia Hunt, and so many more great scientists from all over the world. Here in Mexico we count with names such as Margarita Bernal, Patrizia Calaminici, Annia Galano, Estela Mayoral and so many other. It is hard to make a comprehensive list, and as I said before I could only aspire to have work with the same quality as theirs. The importance of recognizing and promoting women to take a career in computational chemistry will in short be addressed by the FemEx-NL-2017 conference next June 22nd in the Netherlands; their motto is “Promoting female excellence in theoretical and computational chemistry”, certainly a worthy and noble endeavor for a problem far from solved.
Perhaps another good reason for writing this post lies in the image below. It is a true statement but we should analyze the causality for it and fix whatever it is we’re doing wrong because it is certainly not the plumbing:
— David Mobley (@davidlmobley) May 17, 2016
I have a daughter. I want her to be able to do whatever she wants when she grows up without deterrence from unfairness. I want a world for her without labels so she never has the option of playing ‘The Woman Card’. It wouldn’t be fair for anyone around her.
This wont be the last post on this topic. Please share your views in the comments and criticism section. They are all welcome.
It is with great pride that I’d like to announce that for the first time we have a Masters Student graduated from this Comp.Chem. lab: María Eugenia “Maru” Sandoval-Salinas has finished her graduate studies and just last Friday defended her thesis admirably earning not only the degree of Masters of Science in Chemistry but doing so with the highest honors given by the National Autonomous University of Mexico.
Maru’s thesis is for many reasons a landmark in this lab not only because it is the first graduate thesis published from our lab but also the first document on our work about the study of Photosynthesis, a long sought after endeavor now closer to publication. It must also be said that Maru came to this lab when she was an undergraduate student five years ago when I just recently joined UNAM as a researcher fresh out of a postdoc stay. After getting her B.Sc. degree and publishing an article in JCTC (DOI: 10.1021/ct4004178) she now is about to publish more papers that I’m sure will be as highly ranked as the previous one. Thus, Maru was a pioneer in our lab giving it a vote of confidence when we had little to nothing to show for; thanks to her hard work and confidence, along with that of the students who have followed her, we managed to succeed as a consolidated research group in the field of computational chemistry.
More specifically, her thesis centered around finding a mechanism for the excitonic transference between pigments (bacteriochlorophyl-a, BChl-a) in the Fenna-Matthews-Olson (FMO) complex, a protein trimer with seven BChl-a molecules in each monomer, located between the antenna complex and the reaction center in green sulfur bacteria. Among the possible mechanisms explored were Förster’s theory, a modification to Marcus’ theory and finally we explored the possibility of Singlet Fission occurring between adjacent molecules with the help of Dr. David Casanova from the Basque Country University where Maru took a short research stay last autumn. Since nature doesn’t conform to any specific mechanism -specially in a complex arrangement such as the FMO- then it could be possible that a combination of the above might also occur but lets just wait for the papers to be published to discuss it. Calculations were performed through the TD-DFT and the C-DFT formalisms using G09 and Q-Chem; comparing experimental data in CH3OH (SMD implicit calculations with the SVWN5 functional) were undertaken previously for selection of the level of theory.
Now, after two original theses written and successfully defended, an article published in JCTC and more in process, at least five posters, a couple of oral presentations and countless hours at her desk, Maru will go pursuit a PhD abroad where I’m sure she will exceed anyone’s expectations with her work, drive, dedication and scientific curiosity. Thank you, Maru, for all your hard work and trust when this lab needed it the most, we wish you the best for you earn it. You will surely be missed.
As far as population analysis methods goes, the Quantum Theory of Atoms in Molecules (QTAIM) a.k.a Atoms in Molecules (AIM) has become a popular option for defining atomic properties in molecular systems, however, its calculation is a bit tricky and maybe not as straightforward as Mulliken’s or NBO.
Personally I find AIM a philosophical question since, after the introduction of the molecule concept by Stanislao Cannizzaro in 1860 (although previously developed by Amadeo Avogadro who was dead at the time of the Karlsruhe congress), the questions of whether or not an atom retains its identity when bound to others? where does an atom end and the next begins? What are the connections between atoms in a molecule? are truly interesting and far deeper than we usually consider because it takes a big mental leap to think about how matter is organized to give rise to substances. Particularly I’m very interested with the concept of a Molecular Graph which in turn is concerned with the way we “draw lines” to form conceptual molecules. Perhaps in a different post we can go into the detail of the method, which is based in the Laplacian operator of the electron density, but today, I just want to collect the basic steps in getting the most basic AIM answers for any given molecule. Recently, my good friend Pezhman Zarabadi-Poor and I have used rather extensively the following procedure. We hope to have a couple of manuscripts published later on. Therefore, I’ve asked Pezhman to write a sort of guest post on how to run AIMALL, which is our selected program for the integration algorithm.
The first thing we need is a WFN or WFX file, which contains the wavefunction in a Fortran unformatted file on which the Laplacian integration is to be performed. This is achieved in Gaussian09 by incluiding the keyword output=wfn or output=wfx in the route section and adding a name for this file at the bottom line of the input file, e.g.
(NOTE: WFX is an eXtended version of WFN; particularly necessary when using pseudopotentials or ECP’s)
Analyzing this file requires the use of a third party software such as AIMALL suite of programs, of which the standard version is free of charge upon registration to their website.
OpenAIMStudio (the accompanying graphical interface) and select the AIMQB program from the run menu as shown in figure 1.
Select your WFN/WFX file on which the calculation is to be run. (Figure 2)
You can control several options for the integration of the Laplacian of the electron density as well as other features. If your molecules are simple enough, you may go through with a successful and meaningful calculation using the default settings. After the calculation is finished, several result files are obtained. We’ll work in this tutorial only with *.mpgviz (which contains information about the molecular graph, MG) and *.sum (which contains all of needed numerical data).
Visualization of the MG yields different kinds of critical points, such as: 1) Nuclear Attractor Critical Points (NACP); 2) Bond Critical Points (BCP); 3) Ring CP’s (RCP); and 4) Cage CP’s (CCP).
Of the above, BCP are the ones that indicate the presence of a chemical bond between two atoms, although this conclusion is not without controversy as pointed out by Foroutan-Njead in his paper: C. Foroutan-Nejad, S. Shahbazian and R. Marek, Chemistry – A European Journal, 2014, 20, 10140-10152. However, at a first approximation, BCP’s can help us to explore chemical interactions.
Now, let’s go back to visualizing those MGs (in our examples we’ve used methane and ethylene and acetylene). We open the corresponding *.mpgviz file in AIMStudio and export the image from the file menu and using the save as picture option (figure 3).
The labeled atoms are NACP’s while the green dots correspond to BCP’s. Multiplicity of a bond cannot be discerned within the MG; in order to find out whether a bond is a single, double or triple bond we have to look into the *.sum file, in which we’ll take a look at the bond orders between pairs of atoms in the section labeled “Diatomic Electron Pair Contributions and Delocalization Data” (Figure 4).
Delocalization indexes, DI’s, show the approximate number of electrons shared between two atoms. From the above examples we get the following DI(C,C) values: 1.93 for C2H4 and 2.87 for C2H2; on the other hand, DI(C,H) values are 0.98 for CH4, 0.97 in C2H4 and 0.96 in C2H2. These are our usual bond orders.
This is the first part of a crash tutorial on AIM, in my opinion this is the very basics anyone needs to get started with this interesting and widespread method. Thanks to all who asked about QTAIM, now you have your long answer.
Thanks a lot to my good friend Dr Pezhman Zarabadi-Poor for providing this contribution to the blog, we hope you all find it helpful. Please share and comment.
A couple of weeks ago I was invited to give a talk to a small university in southern Mexico called ‘Universidad de la Cañada‘ in the state of Oaxaca, one of the most underprivileged states in our nation. This institution is a rather small one but the work they are doing over there with as little resources as they have is truly remarkable . UNCA offers degrees in pharmacy, pharmacology, food sciences, clinical chemistry and other topics that aim to supply the needed human resources for the various industries that are settled in the region. There is a true feeling of togetherness at UNCA since they have little pieces of equipment yet they are all fully shared among researchers regardless of who received the finance to acquire them. Last year, two of their students came for a two months stay, after which, Alberto and Eduardo got their names on a publication of our research group. It was nice to see them again and even nicer to learn they are about to finish their studies and that they will come back again to our lab in late July.
Every year at UNCA there is a Pharmacology Day on which the students show the results to their research projects during a poster session and listen to lectures by guest speakers from various universities around Mexico. Most of their projects were aimed to the isolation of natural products from local resources and their usage in several kinds of consumer products. UNCA is in a very small town, village I might say, surrounded by mountains and vegetation; the view was spectacular as you may see from the pictures below. Thank you very much to my good friend Dr. Carmen Hernández-Galindo for inviting me to participate and share our work with their students, I hope we may go back again and keep a fruitful exchange between our groups.
During this talk, I took the opportunity to talk about the aforementioned paper in the context of molecular recognition and their in silico design but I think I should have talked more about the computational strategies that are most employed in the pharmaceutical industry. Never mind. I hope I get the opportunity to right this wrong. Still it was nice to give Alberto and Eduardo the opportunity to brag a little about being published authors.
Kudos to Rola Aburto, Dr. Margarita Bernabé, Dr. Rocío Rosas, and all the academic staff at UNCA for their invaluable dedication to teaching science against all odds, I can testify, through the hard work of their students, hat their effort is paying off.
So the World Cup is once again on top of us. I’m not a Football (Soccer) enthusiast but I’ve got to admit that the expectation of such a large and widely covered event is pretty contagious. This year, however, I’m very excited about the inaugural kick-off ceremony because a paraplegic teen will be the one to set the ball in motion, thanks to the use of an exoskeleton developed by the illustrious Brazilian researcher, Dr. Miguel Nicolelis, this patient will not only walk again but also perform a feat of equilibrium: kicking a football. More impressive than the exoskeleton itself is the brain-computer-machine interface since the patient will control the entire process by himself. Miguel Nicolelis is widely known and highly regarded in the scientific community; I’m not sure if he is that famous outside academia, but if he isn’t, he should be. The natural question about Dr. Nicolelis is what is he? Is he a robotics engineer? a neurologist? a programmer? a physician? The answer could be no other than ‘all of the above‘.
And even more impressive than all that, if that’s even possible, is the fact that this huge achievement of technology is presented at one of the most viewed sporting events on the planet. Brazilian organizers could have selected many things to kick-off this event: From Adriana Lima to Pelé; from a Samba line to aboriginal Amazonian people, but instead they chose to go with a scientific and technological breakthrough achieved by one of their own. I wonder if this is a way to tell the world they are interested in investing in science and technology as a way to pave the way of their economical and social development. Brazil is currently regarded as a fast growing nation economically although the social disparity seems to be still quite large. The message I’m getting, at least in principle, is that Brazil is a modern nation with high regard for scientific development on which they will rely their future.
Kudos to the Brazilian organizers who thought of placing this large scientific breakthrough in a sporting event, proving that this world should become boundless and the way to do it is through science.
A bit outside the scope of this blog (maybe), but just too cool to overlook. Augmented reality in chemistry education.
This is a guest post from Samantha Morra of EdTechTeacher.org, an advertiser on FreeTech4Teachers.com.
Augmented Reality (AR) blurs the line between the physical and digital world. Using cues or triggers, apps and websites can “augment” the physical experience with digital content such as audio, video and simulations. There are many benefits to using AR in education such as giving students opportunities to interact with items in ways that spark inquiry, experimentation, and creativity. There are a quite a few apps and sites working on AR and its application in education.
There are 6 physical paper cubes printed with different symbols from the periodic table. It takes a while to cut out and put together the cubes, but it…
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About a month ago my wife and I got invited by our good friend Dr. Ruperto Fernandez (his PhD is in transport logistics and engineering) to his final presentation for a course in managerial skills he’d taken for over six months, and while I wasn’t all that thrilled about waking up at 8 AM on a Saturday, I went to cheer my good friend and show him my sleepy support. His presentation dealt with negotiations and the required skills to master them, and while he agreed that there is a huge amount of talent involved in being a good negotiator, he also pointed out that some basic knowledge of the procedure can go a long way in helping us with little to no talent in achieving the best possible outcome. Basically, a negotiation involves the agreement between a person with something which another person wants; meeting both parties expectations at the fullest extent possible is the ideal endpoint for an iterative give-and-take between them. Or so it goes.
Recently a scandal that involved the biology freelance blogger DNLee, who blogs for Scientific American with the column The Urban Scientist, took place: DNLee was asked by Biology-Online.org to write for them. Then the negotiation started; she had something the editors wanted: her texts. She agreed to do it and presented her fee (second part of the negotiation process: “I got what you want and here is what I ask in return for it“), instead of having an offer made (third part of the negotiation process: “ok, that is what you want but this is what I can give you“) the blogger got a nasty message, which I believe maybe was intended to elicit a response to better accommodate the editor’s demands but that was nothing more than a plain nasty insult: The editor asked if she was the urban scientist or the urban whore (end of negotiation; nobody got anything. Furthermore, feelings were hurt, reputations questioned and the door for future negotiations between both parties was shut completely). If the editor was unable to pay any fee at all then the editor should have tried to convince the blogger of participating for free; I would have offered her a bigger space than a regular blogger, or maybe even invited her to participate as an editor. I’m not sure they have some sort of business model but something could have been arranged. Had this negotiation not met at any point in the middle then a polite thank you could have left the door open for a future time. DNLee has a reputation that allows her to charge for her writings, had it been me, I’d probably had done it for free but because I need more exposure than her who is already famous. Internet support came promptly and hard as can be seen here and here, not that it wasn’t called for, of course!
But the issue, sadly, didn’t end there, DNLee wrote about this in her blog at SciAm, but the post was later on deleted by the editors. Dr. Mariette DiChristina tweeted that the post wasn’t related to science so it didn’t fit in the site. Pressure in blogs and other social networks prompted SciAm to place the article back on the site. Click here to go to the post.
Calling someone a whore is simply unacceptable.
During his presentation, my friend Dr. Ruperto Fernandez, talked about a negotiation he had with a potential employer. According to his account of the process, it ended quite swiftly when he was offered a much lower salary than the one he currently earns. He said the offer had some good points that could have made him accept even 5 to 10% less income respect to his current salary, but much less than that would not help him cover the bills and that was a total deal-breaker. But the talk didn’t end there, some other joint projects were laid for them to work on together and the door is still open for the future when they may be able to match my friend’s expectations as biology-online should have done with DNLee.
It has been a rough couple of weeks for the Scientific American community; first this and now the leaving of a great science writer, Bora Zivcovic whose misconduct has forced his exit out of the popular magazine. So now the aftermath for both issues remains to be seen. Sexism, though, could be found to be a common denominator in both cases: one was a victim of it, the other one is guilty of inflicting it through various instances of sexual harassment. Should this mean that biology-online, Bora Zivcovic and the affiliated-to-the-two-previous parties, the Scientific American Magazine, are to be deemed as unworthy? I hardly think so. None of us is close to sanctity and we all make mistakes, some of them willingly and other unwillingly but we are accountable for each and every one of them nonetheless; but at the same time we should also be able to separate both sides of each story and keep the best of each side while keeping a close eye (and even a loud mouth) about the wrong in each side.
I wish nothing but the best to every person involved in any of these recent events. Why is it so hard for people to just ‘play nice‘? I’ve heard many times this world would be a better place if we cared more for each other, but sometimes it seems that its actually the opposite; that this world would be be better if we didn’t care so much: if we didn’t care about the color of our skin; our gender; our nationality or ethnicity; our sexual orientation; our social status. This brings me back yet again to that presentation by Dr. Fernandez, where he was asked to describe the way he was perceived by others at his workplace and he said he didn’t quite enjoy social interactions so he is perceived as serious and aloof but was always willing to join a new project, so when reached out for one of these he’s all smiles and work. Shouldn’t we all back off a little bit from each other from time to time?
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!
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-benzofuro[3,2]pyrazole and calixarenes will once again act as the potential carriers.
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.
What a happy coincidence -if indeed it was- that #RealTimeChem week happened to coincide with the sixtieth anniversary of the three seminal papers published in Nature on this day back in 1953, one of which was co-authored by J. Watson and F. Crick; of course I mean the publication for the first time of the structure of deoxyribose nucleic acid, or DNA, as we now call it.
You can get the original Nature papers from 1953 here at: http://www.nature.com/nature/dna50/archive.html (costs may apply)
Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid 737
J. D. WATSON & F. H. C. CRICK
Molecular Structure of Nucleic Acids: Molecular Structure of Deoxypentose Nucleic Acids 738
M. H. F. WILKINS, A. R. STOKES & H. R. WILSON
Molecular Configuration in Sodium Thymonucleate 740
ROSALIND E. FRANKLIN & R. G. GOSLING
Nature’s podcast released two episodes (called ‘pastcast’) to celebrate DNA’s structure’s birthday, one of them is an interview with Dr. Raymond Gosling who in 1953 worked under Dr. Rosalind Franklin at King’s College London in diffractometry of biological molecules. If you haven’t listened to them you can get them here at nature.com/nature/podcasts. Of course, the history around the discovery of DNA’s structure is not without controversy and it has been long argued that the work of Franklin and Gossling didn’t get all deserved credit from Watson and Crick. In their paper W&C acknowledge the contribution of the general nature of DNA from the unpublished results by Franklin’s laboratory but that is as far as they went, they didn’t even mention photo 51 which Crick saw at Wilkins laboratory, who in turn got it from Gossling at Franklin’s suggestion. Still, no one can deny that the helical structure with which we are now familiar is their work, and more importantly the discovery of the specific pairing, which according to Gossling was a stroke of genious that probably couldn’t have happened in his own group, but without Franklin’s diffraction and Gossling’s crystallization there was little they could do. Details about the process used to crystallize DNA can be heard in the aforementioned podcast, along with an inspiring tale of hard work by Dr. Gossling. Go now and listen to it, its truly inspiring.
For me it was not the story of a helix, that I was familiar with; it was the story of the specific pairing of two hélices
– Dr. Raymond Gosling
Above, the iconic Photo 51 taken by Franklin and Gossling (have you ever noticed how most scientists refer to Franklin just as Rosalind but no one refers to Watson as James? Gender bias has a role in this tale too) To a trained crystallographer, the helical symmetry is evident from the diffraction pattern but going from Photo 51 to the representation below was the subject of hard work too.
There are million of pages written during the last 60 years about DNA’s structure and its role in the chemistry of life; the nature of the pairing and the selectivity of base pairs through hydrogen bond interactions, an interaction found ubiquitously in nature; water itself is a liquid due to the intermolecular hydrogen-bonds, which reminds us about the delicate balance of forces in biochemistry making life a delicate matter. But I digress. Millions of pages have been written and I’m no position of adding a meaningful sentence to them; however, it is a fascinating tale that has shaped the course of mankind, just think of the Human Genome Project and all the possibilities both positive and negative! DNA and its discovery tale will continue to amaze us and inspire us, just like in 2011 it inspired the Genetech company to set a Guiness World Record with the largest human DNA helix.
Happy birthday, DNA!