Category Archives: Internet
Chemistry and comic books
Science permeates into the collective mind of a society not only through school but also through the form of popular media such as the TV or in the case of this post comic books.
For a long time now, the group of John Selegue and James Holler at the University of Kentucky have a website named as the comic book periodic table of chemical elements. In this clickable periodic table we can browse scans of the pages of different comic books in which the corresponding element is mentioned.
Clicking on each element will display some options for different comic books related to it but for every comic book only the page in which the corresponding element is referenced, is shown, therefore one is not able to read the entire comic book. Nevertheless, for the hardcore comic book fan there are, in many cases, insights to what the page displays putting the comic book, as well as the chemistry within it, in context.
Through the use of the physical properties of chemical elements, many comic book writers have created characters that base their identities in such properties. Also in some occasions, the chemical knowledge of a character helps to the story development. In both cases, chemical concepts are being -literally- illustrated and, ultimately imprinted in the collective mind.
In some cases it seem that there was a deliberate attempt to create a character with a storyline that revolved around the properties of the corresponding chemical element. Such is the case of all the “Metal Men” series in which a group of individuals have super powers related to the main characteristics of each’s corresponding metal. In other cases, such as in mainstream comic books like Batman or Superman, the inclusion of chemical knowledge is brought in by the supervillian who is usually a “mad scientist” trying to take over the world. This vision of scientists with power to enslave the human race probably arose from the atomic era as a consequence of rapid weapon development having the Manhattan project as an imediate antecedent.
The use of popular art forms has the benefit of reaching a larger audience and hence it also has the responsability of not distorting scientific facts into pseudo scientific ones.
Once again this post comes from my memories from the chemistry faculty back at UNAM and the classes of Dr. Raymundo Cea-Olivares who introduced it to us.
Are theoretical/computational chemists real chemists?
Although classifications and rankings do not define the range or scope of work a person/group can do, they are usually popular to look at, unfortunately these views are sometimes misleading in the decision making process, e.g. funding. How expensive is in average our science compared to that of say organic chemists? It indeed depends on the computer facilities at hand and how much are they used, as well as the kind of synthesis performed by this hypothetical org. chem.
The line between theoretical and computational is becoming diffuse, and the branches are increasing (chemoinformatics, chemometrics, bioinformatics and so on.) But since they are somewhat intangible, the results of our calculations seem to often fall into the black box category and hence dismissed or taken with reserves.
There is no doubt that a lot of companies are making a lot of money by selling all kinds of software related to chemistry, from electronic structure calculations to molecular sorting and recognition as well as data analysis. It cannot be denied the enormous amount of scientific effort put in develop such products. Also, pharmaceutical companies make a full use of computational methods as a way to find new drugs in shorter times.
Not too long ago, in the Computational Chemistry List, there was a discussion about whether or not computational chemists were ‘arm chair scientists’ and I’ve been meaning to post on the subject since then. Are we arm chair scientist? maybe so. Is that a bad thing? Of course not! My father is a retired mathematician and I know for a fact that he seldom left his desk, let alone his office. The idea of being an ‘arm chair scientist’ was just obvious for him and there was no need to ever question it. A friend of mine from Mexico told me that there are very few experimental physicists there because for years it was cheaper to make theoretical physics than experimental. I think nowadays students are encouraged to undertake experimental physics in order to balance the ratio.
From my point of view computational chemists can be divided into the following three major categories:
1) Those who develop new theories regarding the electronic structure of molecules as well as new models for modeling its behavior and properties.
2) Those who develop new codes for solving long standing problems. Within this branch we can find also those who develop new basis sets, density functionals, pseudopotentials, semi-empirical methods, force fields, etc.
3) Those (such as myself) who use the products of the previous two branches and apply them into solving problems of chemical interest.
We certainly don’t tackle chemistry the same way our experimentalist colleagues but then again they don’t tackle chemistry the way they used to a hundred years ago. I remember that prof. Raymundo Cea-Olivares at UNAM used to say that chemistry has become ephemeral, since synthesis lasts a day and then the job turns into physics when acquiring and analyzing spectra in order to assess the compound’s identity.
One thing I’ve noticed is that apparently it has become trendy for every research group to develop its own code and those are not good news for people with good knowledge of theoretical chemistry as well as good chemical insight but with poor programming skills.
Just pouring my opinions on the subject…
Knots, fishing and the origin of the universe
Most awful post title ever, I know, but maybe I’m still hooked on prof. Schaefer’s conference from two weeks ago.
I went fishing on Sunday and although my luck was better this time (I caught four fish!) I spent a great deal of time tying hooks, untangling my line from others or even from my own. Whenever the knot became too complicated to solve I just cut the line and tied a new hook or floater. At some point I was wishing there was a tool that could help me to untie those nasty knots and make better ones, I would have settled at least for a recipe! That tool/algorithm exists, of course, and it’s called topology; and within this branch there is a whole area devoted to knots (knots theory.) Of course in topology a knot has no ends, that is, they consist of single loops. This is one of those math areas which found little use during the time of their development but that in time became the framework for complex physical theories such as quantum gravity or string theory, these theories account for the wacky title, of course.
Within topology we come accross graph theory too, which is an everyday chemist’s tool although most of us are unaware of it. 2d representations of chemistry structure are graphs, dots joined by edges. If you look at an old text, the 2D representation of norbornane looks like two fused squares with a methylene in the middle of the common edge. This representation is topologically correct but geometrically incorrect. more complicated molecules were just drawn into texts.
In chemistry, although molecular symmetry is described by group theory (and this in turn connects molecular structure to its quantum properties,) many computational chemistry efforts are conducted on topology and graph theory. For lack of a better example think of SciFinder’s molecule builder tool: in it you can draw a molecule (or a piece of it) disregarding everything you know about structural chemistry, hybridization, the VSEPR model, Bent rules, and so on, and still SciFinder can find related structures to your query because all that it reads are labeled points (atoms) and edges (bonds); it understands the graph, not the symmetry arising from geometry, let alone the molecule. Another example of graphs theory applied to chemoinformatics are those softwares that take a IUPAC name and yield the structure (the graph) or viceversa; what the algorithms do is interpreting or generating graphs once a set of rules were provided.
Among graphs there is a particular kind that is called planar graphs; these can be presented in such a way that no edges overlap each other. There is an online game with which I came across a few years ago and I’m still addicted to it, its name is planarity and it can be found here (NSFW). Molecules are planar graphs but their non-overlaping-edges representation is hardly of any help since their chemical properties rely on their 3D structure.
Now, if I was to set my mind to evil, could we think of people as dots or connectors and their relationships/story-lines as edges and ultimately come up with an algorithm for untangling a lie? It would require a lot of data (the edges) if we were to untangle a lie made by others, but what if we want to weave a life of lies? we know what vertexes are around us and up to some extent the edges between connectors close to us; therefore we could draw bogus edges (lies) provided we could come up with a planar graph in which no two bogus edges overlap. That could be a planar graph plotted on top of a non-necessarily planar one. Definitely unethical but nonetheless feasible from my point of view.
Maybe I should just stick to untie knots in my fishing line next Sunday.
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!
