Category Archives: Science

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.


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 – Happy birthday DNA!

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: (costs may apply)

Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid 737


Molecular Structure of Nucleic Acids: Molecular Structure of Deoxypentose Nucleic Acids 738

Molecular Configuration in Sodium Thymonucleate 740

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 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

Famous Photo 51 by Dr. Rosalind Franklin and Raymond Gosling (Source: Wikipedia)

The iconic Photo 51 by Dr. Rosalind Franklin and Raymond Gosling (Source: Wikipedia)

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.

Modern DNA representation (Source: Wikipedia)

Modern DNA representation (Source: Wikipedia)

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.

Genetech SF, Cal. USA (Source

Genetech SF, Cal. USA (Source

Happy birthday, DNA!

5th Mexican Science and Engineering Fair

Last spring I was invited by The State Council for Science and Technology (COMECyT) to be part of the jury in the 5th Mexican Science and Engineering Fair and now we just had the finals here in Toluca.

For the first part of this competition several projects were evaluated in their originality and relevance as well as their feasibility. The ones that were accepted were later on reevaluated in their progress and now for the actual fair, students from all across the state came to show their results. The scope of the projects I had to evaluate dealt with the use of natural resources indigenous to their local surroundings as starting materials with different applications.

Among the ones that were exhibited today there was a project dealing with substituting wood for cactus in agglomerates. This is a great idea considering the ubiquity of cactus in Mexico and the little attention that is paid to their logs. In another booth, some piezoelectric devices are being plugged together under a sort of mat which will be stepped on by pedestrians generating electricity from their weight, taking advantage thus of their kinetic energy. Once again, on cactae, another team wants to use the resin that comes out of the raw plant as a co-polymerizing agent. I could go on and on about the projects but please visit this link to learn more about it. Below, I share with you some pictures I took from the fair.

Today’s event was attended by the local scientific authorities and by the State Governor Dr. Eruviel Ávila, who in his speech talked about the importance of science and technology development not only in this but in all nation’s states.

Kudos to the local Council for Science and Technology for promoting these events and thanks for including me as part of them.

Institute of Chemistry Library flood – UNAM

If a mind is a terrible thing to waste, then wasting a collective mind is an even more terrible thing. During the past weekend the library at the institute of chemistry suffered a flood caused by a broken pipe just above it, which incidentally happens to be the lab were I used to work as an undergrad student. When it comes to scientific journals, our institute still relies a lot on paper issues for the oldest numbers; we can order them online but it’s just easier to Xerox it at the library if you really need to read that old reference.

This morning the librarians were appalled when noticed not only the huge puddle on the floor but all the books and scientific journals that were dripping water from the shelves. The broken pipe has been fixed and the water on the floor has been mopped. It is now the books the ones that suffer the aftermath of this accident. Not only saving the information was important; wet paper is a great culture media for fungi which in turn could pose a health threat to all users. The administrative staff immediately got to work in recruiting academics and students to help the drying process: “Heal a book!“, they informally called it. Everyone grabbed an item and with the help of industrial blow dryers – the kind we use in chemistry labs to dry wet glassware – and an extraordinary amount of paper towels, each person got to dry the journals page by page.

I got an item that corresponded to the British journal New Scientist, which consisted of about fifteen issues from the year 1980. When I noticed the title in my hand I wanted to switch it. Should we save first those journals with the highest impact factor? or should we work on those that are most relevant to our own research? Should we throw away Chemical Abstracts now that the whole database is online? After all, New Scientist is a magazine which summarizes research that has already been peer reviewed and published; it is journalistic work, not peer reviewed science. But I was afraid to look pedantic so I got to work on drying it.

Kudos to the library staff on organizing in promptu “Heal a book!”

Students as well as the academic and administrative staff drying journals

Each person had their own technique. Some journals had their binding covers still in good shape so they were placed open standing on the floor in front of fans. Some placed paper towels carefully between pages and after a while they would remove them and then use the blow dryer. I thought that if I heated the edges of the paper and thus dried them, capillarity would drive the moisture in the innermost part of each page outwards. Didn’t quite work, at least not in a pragmatic time scale, so I went back to page by page.

I’m glad I did so. That way I was able to find some real pieces of history which could make any scientist nostalgic. For example: I took these photos with my iPod, and if you are by any chance reading this piece on an iPhone, you must find the following  picture about Swedish research endearing.

An ancient iPad or an edgy ‘Etch-a-Sketch‘?

Yes, online doodling games were already a thought back in 1980!

Are you subscribed to this blog? That means you got a notification by e-mail. So what? No big deal! Well, back in 1980 Britain was getting excited over a new form of comunication called the ‘Electronic Mail’ (available only at a couple of post offices). Besides, you wouldn’t have been able to get that message nor read this post on an HP Matrix Machine (you can’t even find a decent link in google about it nowadays!)

But scientists are not all about working, we like games too! So how about purchasing a ‘Hungarian Magic Cube‘ or a ‘Chess Computer‘?

An 80’s sensation!


We also love a juicy piece of gossip. For instance, did you know that John Maddox was a controversial editor for Nature back in the 70’s who, as a student, went into chemistry because if he’d gone into physics he could’ve been drafted by the army in WWII to work on radars? Well me neither. But it seems that we should have known who he was, and now we do.

Sir John Maddox

There were many pieces of science news that nearly kept me in the library all night, if not for the fact that I had to drive 50 miles from Mexico City to my place in Toluca, but the one that captured my attention more than any other was the news of a European dream envisioned more than three decades ago; a dream from a group of scientists about looking for answers, like any other group of scientists, answers that are fundamental for the understanding of our universe and the understanding of matter, back when some of the biggest questions hadn’t even been fully posed, this group of visionaries agreed on taking the necessary steps to build an enormous subatomic-particle Supercollider for the European Center for Nuclear Research, better known as CERN.

The announcement of grand things to come

Back in 1980 I was already alive but I was only two years old. I could barely talk and had no idea what the word ‘future‘ meant, let alone what I’d become when it reached me. Now, even if I’m not a particle physicist I get excited about the news regarding the finding of the Higgs Boson and even if I’m not an astronomer I also get excited about pictures from the Curiosity Rover on Mars. I am a scientist. One out of hundreds of thousands or perhaps even millions, and this is part of my collective memory, the memory of the work of those who paved the road for us, those giants upon whose shoulders we struggle day by day to stand with dignity and against all odds. But here is the thing: those giants are actually made of dwarfs, millions of them; millions of us. Thousands and thousands of papers written, reviewed and published; papers that collectively gather the scientific experience summed up in rigorous experiments both successful and failed.

Preserving the information in those wet journals is important despite the fact you can get them all online. I hope one day a bored chemistry grad student goes to the library and browses old issues of New Scientist and other journals just for fun; they’ll go for a trip down a collective Memory Lane which will remind them that if they can dream it in the present, they can make it come true in the future.

Polarizability and Hyperpolarizability in Gaussian

Calculating both Polarizability and the Hyperpolarizability in Gaussian is actually very easy and straightforward. However, interpreting the results requires a deeper understanding of the underlying physics of such phenomena. Herein I will try to describe the most common procedures for calculating both quantities in Gaussian09 and the way to interpret the results; if possible I will also try to address some of the most usual problems associated with their calculation.


The dipole moment of a molecule changes when is placed under a static electric field, and this change can be calculated as

pe = pe,0 + α:E + (1/2) β:EE + … (1)

where pe,0 is the dipole moment in the absence of an electric field; α is a second rank tensor called the polarizability tensor and β is the first in an infinite series of dipole hiperpolarizabilities. The molecular potential energy changes as well with the influence of an external field in the following way

U = U0 – pe.E – (1/2) α:EE – (1/6) β:EEE – … (2)


Route Section Keyword: Polar

This keyword requests calculation of the polarizability and, if available, hyperpolarizability for the molecule under study. This keyword is both available for DFT and HF methods. Hyperpolarizabilities are NOT available for methods that lack analytic derivatives, for example CCSD(T), QCISD, MP4 and other post Hartree-Fock methods.

Frequency dependent polarizabilities may be calculated by including CPHF=RdFreq in the route section and then specifying the frequency (expressed in Hartrees!!!) to which the calculation should be performed, after the molecule specification preceded by a blank line. Example:

#HF/6-31G(d) Polar CPHF=RdFreq

Title Section

Charge Multiplicity
Molecular coordinates
==blank line==

In this example 0.15 is the frequency in Hartrees to which the calculation is to be performed. By default the output file will also include the static calculation, that is, ω = 0.0. Below you can find an example of the output when the CPHF=RdFreq is employed (taken from Gaussian’s website) Notice that the second section is performed at ω = 0.1 Ha

 SCF Polarizability for W=    0.000000:
                1             2             3
      1  0.482729D+01
      2  0.000000D+00  0.112001D+02
      3  0.000000D+00  0.000000D+00  0.165696D+02
 Isotropic polarizability for W=    0.000000       10.87 Bohr**3.
 SCF Polarizability for W=    0.100000:
                1             2             3
      1  0.491893D+01
      2  0.000000D+00  0.115663D+02
      3  0.000000D+00  0.000000D+00  0.171826D+02

 Isotropic polarizability for W=    0.100000       11.22 Bohr**3.

You may have noticed now that the polarizabilities are expressed in volume units (Bohr^3) and the reason is the following:

Consider the simplest case of an atom with nuclear charge Q, radius r, and subjected to an electric field, E, which creates a force QE, and displaces the nucleus by a distance d. According to Gauss’ law this latter force is given by:

(dQ^2)/(4πεr^3) = QE      (Hey! WordPress! I could really use an equation editor in here!)

if the polarizability is defined by Qd/E then we can rearrange the previous equation and yield

α = 4πεr^3 which in atomic units yields volume units, r^3, since 4πε = 1. This is why polarizabilities are usually referred to as ‘polarizability volumes’.




The use of double zeta quality basis sets is paramount but it also makes these calculations more time consuming. Polarization functions on the basis set functions are a requirement for good results.

As usual, please rate/comment/share this post if you found it useful or if you think someone else might find it useful. Thanks for reading!

Ray Bradbury (1920-2012) and his influence on me…

I was first introduced to Bradbury’s writing in 1989 during my first year in junior high school (here in Mexico that is the 7th grade; I was eleven years old then) by my literature teacher Ángel Molina-Aja at LOGOS School, a progressive institution in southern Mexico City; so now with the departure of the grand master of Science Fiction I can’t help but to think about Ángel and his possible motivations for making us read ‘The Martian Chronicles‘ of all possible books. It is pretty obvious now that his intention was to engage us in literature (prior to ‘Chronicles‘ we read ‘The Hobbit‘) and to make us read something that would in turn make us want to read more and so by reading we would open a world of possibilities to ourselves. His job as a literature teacher wasn’t just to make us learn about literature but to learn how to appreciate it for the values that leaves in our lives, whatever our own inclinations were. As I’ve written before, science fiction is a usual common denominator to us people working in science because we deal with imagining how to bring to life things and ideas that are currently nonexistent. Whether we create new materials with new applications or we come up with wacky mathematical theories that describe the intricacies of the universe, we all have to first set our imaginations free and believe everything is possible. In this way we are sometimes less pragmatical (albeit not necessarily more creative) than lawyers, business people and the like. Education should then be formative, not informative, in order to make an intellectually resourceful population in every area of the human and social development. Here in Mexico the average reading habit is less than 1 book a year per person! and with the upcoming presidential elections and the respective campaigns, it becomes obvious that a poorly read people is a very manipulable one. And the idea of an ignorant population kept in line by the ruling powers through alienating them from literature is the main theme of Bradbury’s other masterpiece ‘Fahrenheit 451‘, in which a fireman is a person who starts fires in order to destroy books (it is widely known by now thanks to this novel that 451 degrees Fahrenheit is the temperature at which common paper ignites itself). In ‘Fahrenheit 451‘ books are banned because they make people unhappy and unsettled by showing them a world of possibilities that they may or may not achieve, so it is safer to just satisfy people basic needs, which include 24 hours of personalized TV programming on every wall of their homes (sounds familiar?), and by doing so they wont question their leaders or their position in society. They just wont have dreams! That’s the bottom line. The many troubles of my country won’t be solved by people reading Bradbury, but if I was engaged into literature by ‘Chronicles‘, among other books from other authors, and by that engagement I was able to discover the world of science and decide I wanted to become one, then the ripple or domino effect triggered by reading, reached its goal; a goal set by my teachers, to whom I will be always most thankful. I wish I could post a picture of my old copy of ‘Chronicles‘ but I guess it’s back at my parents place all worn out. I have to remember taking a picture of it next time I visit my folks. Here is a picture of my old copy of the Spanish translation to ‘Chronicles‘ all worn out thanks to me and my sister, I guess. Thanks to my dad and his ninja-dropbox-skills for getting this picture for me!

My old copy of “Martian Chronicles” in Spanish bought in 1989. Thanks to my dad for taking this picture and using his ninja dropbox skills 🙂

Bradbury’s work and specially ‘The Martian Chronicles‘ romanticized the idea of space exploration. What a huge coincidence, in a sort of a poetic way, that his departure occurred on the same day as the transit of Venus, a phenomenon that will not occur for another 105 years. I wrote earlier on my facebook page that he did not died, that he only went back to Venus. I was close to not posting it for it might be in bad taste, but then I thought that I don’t know what happens when we die and nobody else in the world does either, so this is as valid as any other hypothesis but only more romantically so.

Rest in peace Mr. Ray Bradbury and may this be a thankful testimony for all those hours of rational entertainment and enlightenment.

Paper published in Canadian Journal of Chemistry

A new paper has been published and that is always good news. The paper entitled “Synthesis of new γ-lactones from preactivated monosubstituted pyrazines and TMS–ketene acetals” coauthored by Azucena Garduño-Alva, M. Carmen Ortega-Alfaro, José G. López-Cortés, Isabel Chávez, Joaquin Barroso-Flores, Rubén A. Toscano, Henri Rudler and Cecilio Álvarez-Toledano was a fruitful collaboration between several researchers from within the UNAM Institute of Chemistry and from other labs.

Therein, the lactone formation from pyrazines is analyzed, with some resulting orientations not quite in accordance with the common orientation patterns yield by electrondonor and electronwithrdawing groups. In order to assess the electronic structure of the intermediates and its influence on the resulting orientations, I performed a Fukui analysis based on the Natural Population formalism.

I will come back to this post and expand on the information once I get some more free time, thanks for your understanding. As usual the link to the paper can be located below and it is also available as a pdf file upon request to this author.
Thanks for reading!

Azucena Garduño-Alva, M. Carmen Ortega-Alfaro, José G. López-Cortés, Isabel Chávez, Joaquin Barroso-Flores, Rubén A. Toscano, Henri Rudler, Cecilio Álvarez-Toledano

Canadian Journal of Chemistry, 2012, 90(5): 469-482, 10.1139/v2012-016

On my view about CONACyT’s funding scheme

In science one thing is true and universal: We need funding. Here in Mexico the main source of funding comes from the National Council for Science and Technology (Consejo Nacional de Ciencia y Tecnología, CONACyT) which is an institution that depends directly from the federal government. Over the years different policies have prevailed and right now we are not looking into a good future. I wont go into all the alleged corruption or about the prevailing notion of favoritism within the institution’s scheme for funding research. I just want to write about the process of projects evaluation and what I think are its great shortcomings.

So first, as in any other part of the world, it all begins with a proposal being submitted for evaluation. In this particular case there is a specific application for “Young Researchers”, that is people who are newcomers to any scientific institution in the country, who are in need for a large amount of resources in order to get their own labs going. The notion of an “associate researcher” is not well understood, I think. After the submission is complete and the paperwork validated, the proposal is sent to a few other researchers in the field who either accept or decline to review the project and then are asked concise questions about the originality and relevance of the project; its feasibility; the proponent’s profile about how well suited he or she is to deliver what is being promised, and finally they are asked to evaluate how well justified is the requested budget. The reviewers then turn their comments, and rankings, to CONACyT in which a committee gathers all the data and ranks all the projects. Those projects with the higher ranking get their funding with, maybe, minor adjustments in order to stretch the reach of funding to as many projects as possible. Some other criteria are used, for example researchers at institutions with small budgets have increased chances of being funded than those on a large institution. It is a matter of balance: giving the money to those who need it but that at the same time will sure do more (and better) with it.

So far it all sounds pretty good and fair to me! except there is a problem: Reviewers don’t always do their job properly and sometimes you get to read comments such as

the proponent has no experience in graduating students

well, thats why I clicked the “Young Researcher” button. Some other pearls of wisdom include

the proponent didn’t take into consideration the latest publications in the field he is trying to study

and then he/she enlists references with publication dates posterior to the date of the proposal’s submission! Sometimes our proposals may not be thoroughly well read (or, lets admit, written) and reviewers give you a bad review for omitting things that you indeed covered. But once you get a bad review (from an anonymous peer) there is no turning around, you only find out what they wrote once you have been declined the grant.

My little suggestion: Let the review process be questioned, just once per reviewer and without the possibility of modifying the proposal. That is, once a reviewer emits his or her comments then I could get to read them and address their concerns in a single letter. If I can prove them something so evident as a conflicting set of dates between missing references and the proposal submission’s, then they would have to change their ranking, but without giving me the chance to modify the project anymore as to fit their comments. The process would take longer, maybe, but it already takes more than half a year! a few more months could be worthy if a more fair ranking is obtained.

Science needs funding; not all the scientific proposals deserve funding, true.

On science, sci-fi, fantasy and something called real life

Gina, my girlfriend, is a successful business woman who runs her own company, which implies she has to be pragmatic in order for her business to succeed efficiently. She takes care -probably a lot- of what she says, so for instance she would never say something is awful but rather not nice. Definition through complementarity seems to be the norm in the business world in order to be as likable as possible and thus never driving potential customers away. We scientists on the other hand say things the way they are and hence we are taken by arrogant most of the time. And we are arrogant because we like things right. Even if we understand what you mean with an ill posed sentence, we’ll point out the implications of posing it in a wrong way or just blatantly correct your phrase. We deal with understanding and modifying our surrounding world –the real world, our real world– and, above all things, we love being right! Thus we leave little room for wrong when it comes to other people.

But there is another striking difference between our worlds, one that during this holiday season led our friends (actually my girlfriend’s circle of which I’m now a part) to manufacture and give me this t-shirt as a holiday present:

"Live long and prosper" (BTW I also got a fancy bottle of wine, thanks Poncho!)

Yes. I’m a chemist, I have a PhD and work at a university doing research; that is enough to qualify for The Big Bang Theory cast, right? and if all resemblance is transitive then I for sure spend my Wednesday evenings at a local comic book store, right? Well, wrong! (ha! I loved that one!) But to be completely honest accurate, I do enjoy science fiction a lot. I like the classics such as Asimov and Bradbury as well as Lem and Vonegut. When it comes to cinema I consider myself a huge fan; I prefer Star Wars over Star Trek (if pressed) but particularly enjoyed the latest Star Trek installment more than any of the ones in the new SW trilogy, except maybe for “Revenge of the Sith“. When it comes to fantasy I prefer movies than literature; I’ve never read LOTR and I don’t think I will, but I’m about to re-read The Hobbit during the holidays (I need my leisure reading during the next two weeks).

Back to my pragmatic girlfriend. She doesn’t like sci-fi or fantasy; “fakey” she calls them. For her, achieving suspension of disbelief is nearly impossible and that has made me reflect on where this cliché of us liking sci-fi and fantasy so much comes from.

Science fiction is very appealing to us because allows us to set our imaginations wild and dream about what we could achieve in the future with our own work in terms of technology development (Does Gina dream about building a corporate empire? I’ll ask her tonight). Some of these achievements would involve the verification of wacky scientific theories (think about warp speed in Star Trek and how it implies that speeds faster than light are achievable via the Alcubierre metric in this instance) or the advent of a new set of them. Despite the popular belief, those in the science business have to be very creative people; we cannot simply spend the rest of our careers doing what others have already achieved (although there is an increasing number of people trying) so we all try to stay on the cutting edge even if that only generates a million different cutting edges, some of which become sharper than others. We have to be imaginative, believers of the unbelievable, for only this way we can come up with the technology that eventually makes current sci-fi look fakey. The real world of stock exchange, bills, mergers, negotiations and taxes is very elusive to most of us if not just down boring. The really remarkable thing between us is that both our worlds are able to coexist, and even more so, we support each other in our careers through success and failure, despite the fact we often don’t understand what is going on.

I will continue being the geek within her -now our- circle of friends; I will embrace it and own it. Gina on the other hand will continue being the business woman among my circle of friends from grad school; she will have to keep on nodding when we talk about academia and sci-fi; when we complain about the scarcity of liquid Nitrogen in our labs or we get excited about a new computing cluster with an increasing number of Xeon processors. It’s just a lot of real fun to merge these two real worlds.

Happy holidays, blogosphere! Live long and prosper.

2011 – International Year of Chemistry

PS To wrap things up this year, I’d like to thank to everyone who has liked, shared, commented, followed and subscribed. I want to wish you all a very happy new year! See you all in the future

The (not so) Schön controversy

This title may sound like the one of an episode of the famous geeky sitcom The Big Bang Theory but it is not; it is in fact a far more interesting albeit less fun debate. First of all I want to make clear this post isn’t an attempt to further bash Dr. Schön err I mean Mr. Schön (sorry, I couldn’t help it) but the entire debate raises some interesting questions, specially those regarding the recent outcome of the controversy as well as the forthcoming aftermath, that are worth asking and of course, with some luck, answering.

A little background first: Jan Hendrik Schön (Germany, 1970) got a PhD in physics at the prestigious Konstanz University in his homeland; after that he got a job as a researcher at the even more prestigious Bell Laboratories located in New Jersey USA, where he made groundbreaking discoveries on conductivity, superconductivity, organic conductors and semiconductors. Ironically enough, his conduct was his doom (Sorry again, I couldn’t help this one either. ) Between 2001 and 2002 he published more than 60 scientific papers on these topics, 15 or so of which were published in Science and Nature. Similarities in the graphs led to other scientists to believe the data could have been manipulated which turned out to be the case! Little by little, both journals Science and Nature, as well as other important journals like Physical Review and Applied Physics Letters withdrew some of his papers; others remain under further investigation for their possible withdrawal. Dr. Jan Schön eventually had to come clean and confess his lack of scientific rigor and misbehavior. This and him being fired from Bell Labs could have been the end of the story but in no way was near it. In 2004 the University of Konstanz decided to withdraw his PhD degree to which Dr. Schön appealed on the grounds that his thesis work was performed without any data manipulation or any other sort of ethical misconduct on his part;  finally today after seven years of back and forth lawsuits and appeals the state court ruled against him and the university stripped him from his degree. Dr. Schön is now Mr. Schön. Further details (since this post does not intend to be a repository of others nor to just inform you about the entire gossip) can be found in this Wikipedia article.

So what is this post about then? First of all I’d like to address the obvious questions: Was the University of Konstanz right or wrong about withdrawing his degree? Did they go too far? What are the implications for other scientists? There is still controversy among the scientific community about whether or not the University had any right to do it on the grounds of scientific misconduct on work that they did not fund nor had to do anything with. The matter is fairly obvious, the University of Konstanz does not want to be affiliated with Schön on any level since it will indirectly hurt their reputation. But is someone really thinking that this university is to blame? I hardly think so. Therefore on that side they could have let him keep his degree but on the other side one may postulate that credibility must be sustained throughout our careers just in the same way as MD’s can have their licenses revoked under malpractice. Granted, MD’s get stripped only from the right to legally exercise medicine not from their degree, meaning that in some cases they may recover that legal right instead of having to go to school all over again, although in the harshest cases this wouldn’t help either.

Definitely his conduct deserved strong actions from his employers and the scientific community, in the end almost 30 papers in very prestigious journals had to be withdrawn! He was trying to take the scientific community for a spin! And this is another thing I’m baffled about. Didn’t he ever think that such claims, such amazing claims, would attract the interest of a large number of the most prominent scientists working in the field of conductivity? As if there weren’t billions of dollars invested in those topics worldwide! If he was breaking new ground in organic superconductivity by proving some theoretical predictions, he would have gotten a Nobel prize for sure and that would have attracted a lot more people in trying to reproduce his findings in order to make their own little contributions therefrom. In fact this actually happened! Many laboratories throughout the world claimed to have failed in reproducing his results. I can only imagine those teams feeling frustrated for not being able to get the same numbers/trends in their experiments and clearly getting less and less frustrated when they found out they were not alone and that the number of their companions was growing larger. Had he published his results in some obscure, dubious-quality journal probably nobody would have ever found out, but then Lucent Technologies, the profitable company that runs Bell Labs would have not been happy in funding his research. This in turn raises yet other questions: How come nobody at Bell Labs was able to tell his results were all made up or even just tempered with? Private companies are not run as academic labs, publication of findings go through a lengthier process than in academia, which is normal since private research centers invest a lot of money in developing technologies which will generate enough profit to keep the company running and researching for as long as possible. They also have strict policies about data-recording and experiment-tracking procedures which apply to every researcher in the company; they are not subject to interpretation or to desire, they have to be followed to keep track of all the expensive research done within. The second question I got from this paragraph is about other frauds done in lesser journals which may go unnoticed because the work itself simply goes unnoticed by its own lack of merit. And from this, yet another question is raised and linked to another ongoing controversy: What is the future of peer-reviewing in journal publications? Surely no referee would have tried to reproduce his experiments and I’m sure a large number of data was requested by Nature and Science in order to deem the papers worth of being published (was his answer to this request “No problem!“?) Referees this quality were blindsided by reputations, Schön’s and Bell Lab’s; only until the final users (the readers) noticed similarities between data sets, and noise, in different experiments that the fraud rose to the surface, but noticing those similarities should have been the work of the referees! in fact that is their job! Aren’t they accountable by omission too?

This controversy is not a first, nor will it be the last. The most famous controversy of data tempering that comes to mind right now is the infamous experiment, or more accurately the infamous data selection in Robert Millikan’s experiment for measuring the charge of the electron. In this experiment only the “nicest” data points were used and although inclusion of the entire data set would have not affected the final value of the charge obtained, the statistical error would be increased to 2% instead of 0.5% as he presented it to the scientific community; a much “nicer” error. Of course I’m not trying to compare both cases which are completely apart; selecting data is not as serious as data manufacturing, but they are both just as unethical. Should have Millikan been stripped from his PhD degree and/or his Nobel Prize?

Mexico is not immune to this controversies either. In 2006 three papers authored by the famous Mexican Professor Eusebio Juaristi and his student Omar Muñoz-Muñiz in 2003, had to be withdrawn also on the grounds of irreproducibility from the Journal of Organic Chemistry, Tetrahedron and Tetrahedron Letters. There were serious errors in those papers which led to believe the student had incurred in scientific misconduct but apparently they managed to prove they were simply honest mistakes. Was Muñoz-Muñiz denied his PhD degree? No. In fact he now works as a researcher at Universidad Veracruzana in Mexico. Not a bad gig. I understand he had some problems getting into the National Researchers System which gathers us all researchers in Mexico as an independent entity at the same time that it collects data about the research done in the country. Data seems to be today’s secret word kids! Once again the whole ordeal could have been dealt with if a proper peer reviewing process had been carried out from the very start.

The conclusions: Ethical work, ethical reviews. Is it really that hard?

2011, International Year of Chemistry
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