Monthly Archives: May 2009

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.

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Schaefer, Hawking and God


Last week we had the visit of prof. H. F. Schaefer III here at Babes-Bolyai, that awarded him an honoris causa doctorate for his contributions to computational chemistry, which I must say have been groundbreaking and paradigmatic. Nevertheless his visit is not without controversy. He gave a presentation entitled “Stephen Hawking, the Big Bang and God” which has previously caused some controversy (link) because in it he (somewhat strongly) hints that Christianity is the only valid way/path to a reconciliation between science and religion since widely accepted cosmological theories such as the Big Bang find correlations with creation ideas found in the Bible. He actually stated that the idea of an infinitely old universe is in accordance with Hinduism but not with Christianism. He of course didn’t go as far as to say that because of this reason, BBT is the right one. He said that Walter Nernst and other prominent scientists “hoped” the universe was infinitely old because that would be easier and more comfortable to accept.

The Q&A session was highly predictable: People asking questions such as “how can we believe in the Genesis if nobody was there?“; “aren’t most scientist around the world atheists?“; “who then created God?“. In a nutshell: very cheap attempts to try making Dr. Schaefer contradict himself, as if he hadn’t heard them all before! I imagine some of them thought “I’m going to make him realize God doesn’t exist!” Faith by definition needs no proof, scientists base their conclusions on proofs, so shouldn’t he first proof that God exists and then believe in him? In my opinion he doesn’t have to. Many scientists have separated their religious beliefs from their work in a successful way without feeling contradicted. Schaefer is an exceptionally intelligent person so he conducted his talk in a very intelligent and respectful way, stating every now and then that this were his beliefs and only his.

I myself asked him something of a more practical nature: I started by saying that religious beliefs are a very personal affair and that a debate on the existence of God could take forever “If so many scientists are tracing parallel lines between science and the Bible, doesn’t threatens the work of non-christian scientists and exposes them to be segregated from main stream science?” The answer I got was somewhat vague: “Science, as we know it today, was generated by Christians and has so far been extended to everyone, so now that [science] is out there everyone can be a part of it”.

Of course anyone is entitled to whatever religion he/she wants, but is it wise to preach, however subtly, from such a position? Religion is a very personal affair and I think that such a talk may influence young science students into follow non-scientific endeavors such as this intelligent design theory we have heard a lot about in recent years. Then again it would be tough not to fall into the intolerant category if one is to ask such speeches to be banned from universities all together, since a university should be the perfect place for respectful and insightful debates. In this same way, the work of scientists shouldn’t be scrutinized under a religious lens that could ultimately segregate the work of those who don’t agree with us.

Believe and let believe; that’s more my philosophy. Lets be inclusive and open minded, religions wont vanish, just as skepticism wont vanish either. Let both be starting points for ideas to arise so by hard work we ultimately achieve a full understanding and control of Nature (yes, with a capital N).

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!

On the popularization of science


Although the popularization of science is an important task, I’ve always believed it’s not always addressed properly and way too many attempts have been made to emulate Carl Sagan’s COSMOS TV show. Many misconceptions arise from a wrong approach to the matter, and the two more susceptible scientific areas to such misconceptions are quantum mechanics and relativity, mainly because its hard to trace parallelisms between them and the every-day-phenomena in such a way that any layman is able to understand.

Everyone has heard how time elapses when moving close to the speed of light, and since a (regular) heartbeat could be considered a clock it is said that a person would stop aging (as if any other physiological process was also periodical.) What about distances becoming shorter? if we accept that our femurs (or any other bone for that matter) could be used as a ruler then we’d become short during the same trip! of course this latter effect has little impact on popular conceptions, e.g. science fiction narrative.

When it comes to QM the things become even harder to tell since there are some quantum effects that have no classical correspondence such as spin. It is very hard to explain QM to lay people without recurring to Schrodinger’s cat or just stating that its a theory of probable outcomes. True dangers arise when pseudo scientists come up with ridiculous attempts to merge science with superstitions. Such was the case of that movie “What the *bleep* do you know?” in which is said that molecular structure can be influenced by external human stimuli such as mood changing!

Now, chemistry is not immune to this sort of phenomena. During the last few months, German astronomers reported having observed two organic complex molecules in space: butyronitrile and ethyl formate. The latter is the fragrant substance in raspberries, of course this last fact was never adressed by the astronomers at the Max Planck Institute. Nevertheless, a journalist for The Guardian who picked up on it, wrote a paper stating that our galaxy smells like raspberries! Of course the statement was made with the intention of using it as a hook for readers, when the real importance of such a discovery is the presence of complex organic molecules since that implies there is a possibility of finding other molecules such as amino acids, but if the point is not delivered all the way home then a layman could keep only the fact that our galaxy might smell like raspberries.

Never been to fond of teaching, I hope in the near future science becomes more popular, just not cheapen; and for that more and better education is needed at all levels possible throughout the world. My fear is that superstitions and cults spread faster than education since, of course, the latter takes time and dedication from people, not to mention talent too.

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