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Virtual Conference in Computational Chemistry VCCC-2014 (1st call)


So many things have happened since I last updated this blog but I will come to write on them when appropriate. Right now I’d like to share an invitation by Prof. Ponnadurai Ramasami from the University of Mauritius to the upcoming Virtual Conference on Computational Chemistry from the 1st to the 31st of August. Deadlines can be consulted here and the most important is the abstract submission on June 30th. This conference is part of the official celebrations of the International Year of Crystallography so talks involving experimental determination of electron densities will be well suited.

I participated in the latest edition and I must say it was a very enriching opportunity to learn from so many other researchers from across the world without leaving my desk. I already know what my talk will be about, now that we are so close to finish and submit a paper on the absence of reactivity for an anti-aromatic set of molecules. (I think I’ll call it “The reactivity of molecules that never existed [but that maybe should have.].) All talks are sent either as pdf, powerpoint presentations, youtube videos, etc. and Q&A are done over e-mail.

So this is a calling to other computational chemists out there who want to participate in this virtual conference. Kudos to Prof. Ponnadurai Ramasami and lets hope we can crystallize his visit to Mexico during 2014 the International Year of Crystallography (pun intended) and here’s to me going sometime to Mauritius!

Negotiations gone wrong and other recent scandals


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. 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 waived 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 waive her fee, 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 but 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?

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.

Webinar with Dr. Erik Lindhal – NVIDIA+GROMACS


Thanks to Devang Sachdev from NVIDIA for bringing this webinar to my attention.

The future of computational chemistry seems to be written in CUDA for GPU’s specially when it comes to Molecular Dynamics; as such, NVIDIA has gone through great lengths into introducing scientific computing methods for GPU’s. I still have a pending review of a test drive that people at NVIDIA and EXXACTCORP kindly allowed me to run but that is the topic of the next post.

Next Thursday, April 4th, 2013 from 9:00 AM – 10:00 AM Pacific Standard Time there will be a webinar in which Dr. Erik Lindhal at Stockholm University and NVIDIA will discuss latest GPU-acceleration technologies available to GROMACS users; more specifically the latest accelerated version of GROMACS 4.6, which features are supported, it’s installation and use, and how it performs with latest NVIDIA Kepler GPUs.

Register here: http://goo.gl/0HtqJ

Please register and check your local timezone to avoid delays. I will register as soon as I finish typing this. Thanks once again to Devang Sachdev for all his help, patience and trust in this forum.

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!

E-chess

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.

www.CCIQS; The (not-quite) official website


The Joint Center for Sustainable Chemistry Research (Centro Conjunto de Investigación en Química Sustentable) was born in 2008 as a project between the Institute of Chemistry from the National Autonomous University of Mexico and the Chemistry School from the Mexico State Autonomous University aimed to the development of research in green and sustainable chemistry as well as that of human resources trained in the same areas.

I have found through the statistics page in this blog that CCIQS is a somewhat popular search term but unfortunately there is still no website available due to some technical dificulties. Therefore I here upload the link to our proto-website (only Spanish for the time being, sorry)

I hope this helps people find some info about what we do and how to get in touch with us. Opportunities for scholarships are available both for graduate and undergraduate students. If you are interested in working with us, please get in touch with the researcher of your choice and ask for any available positions; we look forward to having more students to interact with!

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/

The power of “idle” international scientific cooperation


What if you could convince people to help you doing your research on their spare time? What if you could convince a million people to contribute to a specific scientific effort without the need of recruiting them yourself? Even better if you can get all these exo-collaborators without making a huge dent in your budget, which sometimes is just impossible even if you are willing to do it. The world is an interconnected global one these days; millions of voices sound through the web which makes it hard for yours to stand out. As an interconnected entity, communicating to a large mass has become feasible but it comes with a price: you need to be attractive! That’s right, you can get a million people to help your scientific efforts, its called crowdsourcing (think about wikipedia for instance), but you have to make it rewarding in some way, and since you are trying to convince them to work for you in their free time you have to make it look like something they’d do on that free time; So why not making it a video game?

There are nowadays some serious games which are nothing more than an internet-based platform in which tons of data are loaded and accessed by many users who analyze them while being scored on their achievements in many different ways according to the rules of each game. Remember that famous NASA screensaver (SETI@home) which used the idle time on your computer to crunch data from the SETI (Search for Extraterrestrial Intelligence) project; that is a more passive example of exo-collaboration simply called distributed computing, since the user has to do nothing but allowing the entrance of data into their computers for further processing.

Fold.it is a videogame (that actually began as a distributed computing screensaver called Rosetta@home) that allows you to play around with a protein and fold it in many different ways while you score points according to the conformer’s plausibility. Obtaining the native tertiary (and even the secondary) structure of a protein from no other information than the primary structure is extremely difficult given the enormous amount of available degrees of freedom. Molecular dynamics alone is unable to predict the native tertiary structure of the protein; the number p of possible disulfide bonds present in a protein is p = n!/[(n/2)!2^n/2]  where n is the number of cysteine residues available, plus computers know nothing about proteins or enzymatic catalysis so a hand from us fellow humans and our chemical insight is widely needed. Therefore our previous knowledge of chemistry, biochemistry and the nature of related proteins can help us help those programs in finding the best possible answer to ‘how does this protein look like in 3D space?’ but since this human-helped process is slow and cumbersome you need thousands of people working on it a great deal of time; almost as if every person playing with the same structure was a single core in your computer. Fold.it thus, is a sort of protein self docking, if you will, in which players are ranked according to their skills and rewarded according to how well your structure complies with three simple rules: 1) lack of voids (packing) 2) keeping the orange hydrophobic chains unexposed to the aqueous exterior and 3) avoiding clashes. Scoring functions for these three concepts are calculated and then yield a score for the player which is then ranked to other players folding the same protein (or to other players in their overall performance).

Image via Fold.it wiki

Fold.it has already collected some major success stories such as the one published on Nature Structural & Molecular Biology by David Baker (founder of Fold.it) et al. on September 2011 (doi:10.1038/nsmb.2119) in which players helped in solving the crystal structure of a protease from a retrovirus which causes AIDS in monkeys. The determination of this structure had already taken 15 years of work with only partial success; but the data was available in Fold.it for only three weeks when the appropriate match to the diffraction experiments was found! This case alone has stirred too much attention and for a beautifully written piece about it, you can check this article at the Discover Magazine by Ed Yong.

Other such examples of crowdsourcing in scince, more specifically in astronomy, are Galaxy Zoo and Moon Zoo in which thousands of images from the Hubble telescope and numerous moon probes are made available for users to sort and classify. The aim of Moon Zoo is to study the amount, shape and occurrence of craters, which basically never erode unlike those on Earth. This analysis will let us know more about the origin of our natural satellite and ultimately about the origins of our solar system.

To the participants in this specific kind of scientific crowdsourcing the term Citizen Science is applied and even publications such as the Scientific American magazine host a section where you can call out for volunteers in your projects. Some sort of classified ads for the lonely scientists in their labs in search for “idle” hands that can make a significant contribution to science. Some Citizen Science projects are intended for kids and teenagers as a way to get more people interested in scientific disciplines by engaging them directly in activities with a measurable progress of their own contributions. It is worth mentioning that projects like Fold.it, Moon Zoo and Galaxy Zoo are developed in a way that can be used by people with no expertise in the field in order to recruit as many people as possible just to perform a very specific task, proving thus that the human brain is a powerful and beautiful machine whose insight isn’t equaled by any artificial system, yet.

Well, it is now time to go back to work before I’m deemed a permanent exo-collaborator by my bosses. Just a final thought: What were our mothers saying about us playing too much with our video games?

2011, International Year of Chemistry

As usual please share your thoughts in the comments section, rate this post and let me know that you are out there reading this.

The Future We Create (Part II, The webinar)


The Future of Sustainable Chemistry

As part of the ongoing events of the International Year of Chemistry, I was interviewed last month for a webinar titled “The Future of Sustainable Chemistry” which in turn is part of a broader series of webinars called “The Future We Create“. These events are sponsored mainly by the DOW Chemical Co. and organized by the 4goodmedia organization as a way to stir up the debate among a broad spectrum of scientists, entrepreneurs, politicians and pretty much anybody willing to pay attention, about important issues of our time. In this webinar, the role of chemistry as part of the solution to the sustainability problem, was explored. Here is my contribution to the event

The official site and full length video (about an hour long, 30 speakers) is available at Future We Create. I strongly recommend the talks of Peter Adler, Paul Alivisatos, Harry Gray and Martyn Poliakoff, which were some of my favorite.

Despite the popular belief, chemistry is not to be feared but to be learned. We can’t get rid of chemicals, every product we use, every service we hire, requires at some point to cross paths with the chemical industry. But the chemical industry needs to address the problems it generates in our environment on the long run and it is there where green and sustainable chemistry come not as a new branch of chemistry but as a way of doing chemistry.

Needless to say chemistry has transformed our world; and it can do it again.

 

2011, International Year of Chemistry
http://www.chemistry2011.org
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