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Stop SOPA


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

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

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

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

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

of speech over the Internet.

http://sopastrike.com/strike/

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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

The Future of Sustainable Chemistry; The Future We Create (Part I, invitation)


I was recently invited to participate in a series called The Future We Create. This event is the third installment in an ongoing conversation (sponsored by Dow Chemical) to explore how chemistry can collaborate with other sectors and concerned citizens to solve humanity’s most important challenges. The title of this installment is The Future of Sustainable Chemistry which will be aired next Tuesday! An official invitation follows. Thanks and I hope you all tune in (I don’t know if the video will be available on their site after the broadcast).

I am happy to invite you to The Future of Sustainable Chemistry video conference on August 16 at 11am EST, where I will be one of the speakers examining the role chemistry can play in a sustainable future.

In 60 minutes, The Future of Sustainable Chemistry will feature 30 experts from leading universities, government organizations, businesses, research institutes, and non-profits.The topics covered in the webinar will include:
·      The History of Chemistry and the Chemical Industry
·       Defining Sustainable Chemistry
·       Barriers to Sustainable Solutions
·       New Potentials that Could Solve Global Challenges
·       Collaborations, Working Across Sectors and BordersThe virtual conference will help participants from around the world gain a greater sense of the central role chemistry plays in all of our lives, as well as the direction it must take to catalyze a sustainable future.

You can register here:  http://www.futurewecreate.com

It is sure to be a lively conversation. I hope to see you there!

Thank you all for reading and making this blog a successful one

2011, International Year of Chemistry

http://www.chemistry2011.org

Fresh new look!


A new look was needed in this site! and some more changes will be made in the next few days. A new page was added with the topics of the courses I’ve taught here at UAEMex, namely QSAR and Molecular Modeling. Another page was added for you all to leave questions which are hard to fit into other places of this blog. The idea behind this page is just to have a more organized site, since sometimes there are questions on odd places such as the About Me page or something like that.

This blog will slowly transform into a site for my incipient research group, however the blog will always be an important part of this site and will continue to be the front page, at least for now.

Have any comments or suggestions? please let me know in the comments section!

2011, The International Year of Chemistry (IYC 2011)


IYC 2011In April 2006, during a IUPAC Executive Committee meeting, the idea for an international year of was first discussed. From that meeting a IUPAC committee was appointed to work along with UNESCO in the creation of the event and finally during 2008, the year 2011 was officially designated the International Year of Chemistry (IYC 2011); additionally 2011 marks the 100th anniversary of the Nobel Prize awarded to Madame Marie Curie so the IYC 2011 will also be devoted to celebrate the contributions of women to science in general and not only to chemistry. Furthermore, 2011 is also the 100th anniversary of the founding of the International Association of Chemical Societies so the benefits of international scientific cooperation will also be highlighted.

The International Year of Chemistry represents a great opportunity to celebrate, highlight and raise awareness about the extraordinary achievements of chemistry and how it has mold the way we live. The IYC 2011 motto is “Chemistry- Our life, our future”. To me this motto reflects how chemistry will help to solve the current problems our planet is going through (from global warming to alternative energy sources); I work at a research center that is ultimately supposed to be devoted to research in sustainable chemistry, so the appeal is huge! The main goal of the IYC 2011 is to increase the public appreciation of chemistry by reaching out for the general public (in the end, us chemists are already interested in chemistry) in a wide variety of activities that will range from conferences to hands-on experiments and other forms of interactive performances for people of all ages. Everyone can get actively involved by just visiting the official website (see below)

We live in times where science surrounds us yet people fear it, distrust it, argues it without foundations, school boards in first world countries dare to promote religious-like factoids in education. It is our duty as scientists to raise awareness about the importance of chemistry to the technological and cultural advancement of the human race, at least so next time some TV ad announces a chemicals-free product people raise their eyebrows.

Like every well respected institution around the world, here at UNAM we are organizing a series of events directed to celebrate the International Year of Chemistry. I’m already trying to organize a visit for some of the most brilliant people I had the pleasure and honor to meet and work with at Babes-Bolyai in Romania, hopefully we’ll build some academic bridges between our two institutions. Also a series of books on different aspects of chemistry (from the very scientific to the more philosophical kind) will be published by our university.

I encourage you to promote the events in your local scientific community, but also to raise awareness within your non-scientist friends. I will sign all my emails, twits, blog posts and Facebook updates with something like ‘2011, International Year of Chemistry’. What about you? Chemists of the world: Get involved!

Thanks for reading!

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

The Chuck Norris of chemistry


It is widely known by now, the existence of a list called “The Chuck Norris facts” in which macho attributes of this eighties redneck action hero are exacerbated for the sake of humor. The list includes such amusing facts like:

  • “Chuck Norris doesn’t eat honey, he chews bees”
  • “When Chuck Norris does a pushup, he’s pushing the Earth down”
  • “Chuck Norris counted to infinity; twice!”
  • “There is no evolution, only a list of creatures Chuck Norris allows to live”

This last one is funny also because Chuck Norris is a Born-Again-Christian who doesn’t believe in evolution. The list is very funny although the original site has become plagued of not so good ones thanks to uninspired people with web access.

A not so old list, and definitely funnier for us people in the science business, is “The Carl Friederich Gauss list of facts“, which includes gems like:

  • “Gauss can divide by zero” (funny although a bit obvious, right? well this is warm up)
  • “Gauss didn’t discover the normal distribution, nature conformed to his will”
  • “Gauss can write an irrational number as the ratio of two integers”
  • “Gauss doesn’t look for roots of equations, they come to him”
  • “Gauss knows the topological difference between a doughnut and a coffee mug”
  • “Parallel lines meet where Gauss tells them to”.

All these facts imply one thing: impossibilities being allowed to one paradigmatic character for humor’s sake. What could be considered an impossibility in chemistry by now and who could be the one to bear Norris’ fame? Who could be deemed as the Chuck Norris of chemistry?
The impossibility of synthesizing noble gas compounds comes to my mind as the historical impossibility in modern chemistry most imprinted in chemists minds since its written in Pauling’s textbook and is supported by Lewis’ theory; yet Bartlett achieved their synthesis during the 60’s! Chemistry is a science which generates it’s own study matter and as such, impossibilities become challenges. What are the current challenges in chemistry? what is the direction our science is taking or even worse that it should be taking?

So here is my first attempt at emulating the list of facts in the chemistry field and my chosen one is Roald Hoffmann!

  • Roald Hoffmann can make a C atom hybridize d orbitals into its valence shell
  • Roald Hoffmann drinks AlLiH4 aqueous cocktails
  • Roald Hoffmann can stabilize a tertiary carbanion and a primary carbocation
  • Roald Hoffmann can analytically solve the Schrödinger equation for H2 and beyond (of course)
  • Roald Hoffmann denatures a protein by looking at it and refolds it at will
  • Roald Hoffmann always gets a 100% yield
  • Le’Chatellier’s principle first asks for Hoffmann’s permission
  • Roald Hoffmann once broke the Periodic Table with a roundhouse kick
  • Roald Hoffmann can make a molecule stop vibrating at absolute zero; it’s called fear!
  • Born-Oppenheimer’s approximation is a consequence of nuclei being too frightened to move in the presence of Roald Hoffmann. Electrons? they are just trying to escape
  • Roald Hoffmann’s blood is a stronger acid than SbF5

A pretty lame attempt I admit. Who is your favorite chemist in history and why? Try to come up with your own Chuck Norris of Chemistry list and we’ll share it here in this site.

As usual thanks for  reading (yeah! the whole three of you)

The Chemical blogspace (Cb) has ranked this blog!


I just recently found out this very blog of mine was found and ranked by the Chemical blogspace as number 96 (out of about 250, before you ask). I still don’t know how do they do the math but it seems it has to do with the number of clicks a blog gets over a certain period of time and relating that somehow to the number of new posts over that same period. The Chemical blogspace is a blog which retrieves information from other chemistry blogs on the Internet and gathers it in a way that allows one to search by author, blog, topic or even molecule. The following link is to the ranking of my blog within Cb.

Why isn’t it retrieving my photo or why do all posts appear in the feed without the proper title but with my fullname instead? I have no idea!

Be that as it may, I’m very happy to know this rather neglected hobby is out there, is getting read and has even become a small Internet resource. I call it neglected because my posting rate is about 1 post/month. Some posts have become very popular, such as the ones on NBO analysis and their visualization and the one on PCM calculations and troubleshooting. Some have never amounted to much like the one on my thoughts about baseball or the relationship between knots -through graph theory- and chemistry. Some rants I like a lot like the one on the invention of the wheel and some got posted without proofing (and they remain shamefully so) like that on basis sets. During the first few months the number of visitors was somewhere between 40 to 60 visitors per month, now I don’t have less than 1700 a month! I now get a lot of questions from -mostly- students worldwide, and although I can’t always help them -sometimes not even reply soon!- I’m glad to be taken into consideration. It’s interesting to get these questions since in the vast majority of them you can tell they actually read the posts first; this means this is people actually trying to get something done! I don’t think I’ve ever had a question that requires an RTFM answer, thank goodness!

This ranking makes me think it could be worth the while to post things more often about my own work; also a good redesigning of the site is due in order to make it a site and not just a blog. Who knows? maybe I can climb higher in the ranking by the end of this year 😉

Thanks to everyone who has ever clicked, read, rated and commented the entries!

Cheers!

The Computational Chemistry List


The Computational Chemistry List  (CCL) is a web based forum in which is possible to discuss basically every aspect regarding computational chemistry, from fundamental concepts to technical assistance, the latter being the most popular form of posting. The value of CCL to the work of computational/theoretical chemists cannot be under-stressed since literally thousands of researchers and students around the world share their knowledge through it on a daily basis. The list is maintained by Dr. Jan Labanowsky who in some occasions has undergone severe problems to keep it running. Fortunately for us, he has always succeed in it. For example, in 2007 when bad weather struck the Ohio state where he lives he kept the CCL servers running with the help of a couple of gasoline generators. These servers are located at the basement of his house so it doesn’t really get more personal than this.

Of course, as with any other forum, the CCL is not immune to host controversies that later become e-mail wars although they have never left the original scope of the list nor the respectful framework expected among scientific researchers. But the CCL is not only a forum or an online comunity, it is also a repository for papers, codes, technical data and even a board for posting conference anouncements and job offers.

A very nice post about the importance of CCL and the work of  Dr. Labanowski can be found here at Dr. Alejandro Pisanty’s blog. Dr. Pisanty has been the director of the Academic Computing Center at UNAM, Mexico, for quite a number of years now, and was involved in the development of the CCL back in the early nineties.

The CCL has been running since 1991 and is a great example of how the Internet  isused to support research. I wonder if it’s possible to use the tools of web2.0 for research much in the same way as the CCL has done? Long live the CCL!

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