Category Archives: Random thoughts
Prof. Dr. Ioan Silaghi-Dumitrescu (1950-2009)
Yesterday, on December 25th prof. Silaghi passed away. He leaves us all, his students, co-workers, friends and relatives with a deep hole in our hearts. We all witnessed what a hard year he had in terms of health and we are solely comforted by the thought of him not suffering anymore. I hereby send my condolences to his wife, children and grand children hoping they find comfort and peace. I guess I could write about the director of the faculty of chemistry; about my boss; about my co-advisor during my grad student years but instead I want to write about the man and friend who in no little way touched and changed my life.
I met Ioan in 2002 during his last visit to the Chemistry Institute at UNAM in Mexico City when he came along his wife, Prof. Dr. Luminita Silaghi-Dumitrescu, to give an introductory course on molecular modelling. For a long time, he had been close to Dr. Raymundo Cea-Olivares, director of the institute, who at the time was also my advisor in my first year in grad-school; back then I was intending to work in the realm of inorganic chemistry and although I was becoming increasingly interested in theoretical chemistry, Ioan’s lectures were partially responsible for me changing my main research topic. It wasn’t only until 2005 that I had the opportunity to go and work with him for 6 months at Babes-Bolyai in Romania. Although his schedule was usually tight he always found time to talk, however briefly, with his students. He was always present at his students’ birthday parties, ready to sing ‘La Multi Ani’ or to tell us all a new joke. A youthful and warm man, Ioan also found time that summer to help me out with my immigration problems. A couple of years later he fought and won a huge battle against cancer; apparently it came back, this time for good.
After I left he offered me a postdoc position which I kept postponing until last year when I finally took it and although we didn’t see eye-to-eye on some things, I’m glad I took this position and was able to work with him once again. He always believed in me and my work, and for that I will always be most grateful to him. I will miss one of my mentors, a dear friend, a truely warm and loving man. May he rest in peace.
La revedere Ioan, ne vedem dincolo o zi.
-
- Ioan Silaghi Dumitrescu and I (2005)
-
- Ioan Silaghi-Dumitrescu and his wife Luminita in their summer cabin (2005)
Wrapping it up!
This year went by in a heartbeat. A lot of things happened and some nice research was performed. I especially enjoyed the summer in Hungary and working at Pecsi Tudomanyegyetem. Now the year is coming to an end and so is my contract as a scientific researcher at the Babes-Bolyai University, unfortunately the lack of further funding prevents me from extending my stay here for another year (damn crisis!), so now I’m in search of a new job whether it is in academia or in the industry, the important thing for it is to be challenging and interesting, also well payed, of course. I’m keeping my options open and I already have some which I will look into very carefully. I’m not going to jinx them by posting them here 
Even though the year and my contract are almost finished I’m far from being free of work. I’m currently working on the final details of a couple of papers concerning this year’s work; next week (1st December) I travel to Skopje, Former Yugoslavian Republic of Macedonia, to lead a workshop for undergrads on computational chemistry; finally, on the last day of my stay in Romania I will give a small lecture for masters students on Molecular Dynamics. Aside from all that we have to count the numerous good-bye visits to friends and colleagues.
Romania is a beautiful country with a rich cultural heritage. Unfortunately there are still a lot of struggles within the ruling forces hindering the progress of the country as a whole. Romania has been a constant presence in my life for a few years now since I came here as an graduate student for a research stay in 2005. I encourage everybody to put this country in your future tourism list and take the Transylvanian tour as I call it (Bucharest-Sinaia-Brasov-Sibiu-Sighisoara-Cluj Napoca); for those interested in skiing there are marvelous stations in Poiana Brasov and in Straja near Petrosani. Here’s to my second home, my heart remains in Transylvania, multumesc Ardeal!
Changes are always thrilling, lets see what the future has for us in the short term. In the mean time I want to wish everybody to have happy winter holidays and enjoy them with your loved ones.
Peace
Back to Romania
After two months of working at Pécsi Tudomanyegyetem in the research group of Prof. Kunsági-Máté Sándor, I go back now to my previous office at the Babes-Bolyai University in Cluj-Napoca, Romania. Working here at Pécs has been a stimulating experience as well as a very productive one. We managed to obtain enough data as to prepare a couple of papers, which should be ready for submission in about a month. Several calculations on the hosting properties of a selected series of calixarenes were performed in order to further shed light on their skeletal properties with and without guests. NBO calculations were also carried out to assess the bonding properties within these molecules. Most calculations were carried out at the HF/6-31G(d) level of theory and only some DFT (B3LYP) were performed for comparison only. We expect to further understand the mechanisms by which calixarenes work as molecular recognition agents.
Be this a public recognition of the Hungarian hospitality, specially that of Prof. Kunsagi Sandor.
Kösönöm!
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.
Explaining Entropy can be a mess…
Another scientific concept that is hard to grasp by laypeople and that to my opinion has been the center of much distortion in the chemistry classroom, is the thermodynamical function Entropy, S.
More often than not, S is said to be a measure of “disorder” and people just take it! If one was to define disorder then one would have to also define order: Is my apartment too entropic? what about my life? Does nature understand order in the same way as we do? How do we understand order inside a living cell where many molecules and organelles are floating around? If indeed S was a measure of disorder then, why is it important to measure it?
Entropy in a nutshell. There have been many attempts to define S in a way young students may understand it, yet tracing parallelisms with ordinary every-day-life concepts is hard and often leads to miss conceptions. A student of mine once asked: “if entropy is always increasing, how come bodies tend to cool down?” he meant to ask how come the translation motions of a molecular ensamble tended to decrease (and with this achieving “order”.)
Prof. Mayo Martínez-Kahn at UNAM in Mexico wrote a very interesting paper about Entropy in the local journal of the Chemistry School, “Educación Química”. The paper was entitled “The tombs of Entropy” as a reference to the widely known fact that in Boltzmann’s tomb his famous equation relating Entropy to the partition function Q, is engraved. Prof. Martínez then ventures in imagining how would other tombs from people who have made contributions to the concept and notion of S would look like. I remember distinctively the one of Sadi Carnot’s in which his famous thermodynamic cycle was displayed.
Entropy in so many words is a function that describes how many different energy levels are available in a thermodynamic system. The more levels, the higher the entropy. It also describes the spontaneity of a process to occur since in nature a system always tends to undergo changes that increase its entropy along with that of its surroundings.
How come Gibbs’ free energy or Helmholtz don’t cause such confusions? my guess is because nobody has attached an every-day-word to them!
PS. It is still important to make scientific concepts permeate into the general audience. Recently decesead comedian George Carlin mentioned Entropy in the following video…
Moving out
As part of the research project I’m working on here at the Babes-Bolyai University in Romania, I must now pay a visit to prof. Sandor Kunsagi-Mate in Pecs, Hungary. I’ve met prof. Kunsagi in several occasions before and I’m looking forward to working with him in his research team, although unfortunately he will have to leave next week to the far east to check on some of his multiple collaborations around the world. I’m also looking forward to use their computer facilities which I think are physically located in Budapest. Living near Budapest is something I’m also very much excited about since it’s one of my favorite cities in the world.
I haven’t read much about the University I’m going to, other than it’s the oldest university in Hungary dating back from the days in which King Matei Corvin ruled the Hungarian Empire. King Mathias was born in Cluj-Napoca, by the way. That’s a good 600 years now!
It’s always exciting to start anew in a completely different environment with a new research team. This time my chances of learning a bit of the language are pretty slim. In fact I’ve heard a lot of Hungarian here in Cluj and I haven’t learned too much, other than some isolated words.
Despite all the problems we face on a daily basis here at UBB I will miss Romania while I’m gone; it could be for a month or two. Romania has crawled under my skin, so even if I -often- complain about their ways and customs, it is now a part of me and I think I’m starting to feel homesick.
Pecs will be a nice adventure, I’m sure.
Wheel? I think knot!
Once again an awful title. This post follows my previous one on graphs and chemistry, and it addresses an old idea which I have shared in the past with many patient people willing to listen to my ramblings.
It is a common conception/place to state that the wheel was the invention that made mankind spring from its more hominid ancestors into the incipient species that would eventually become homo sapiens; that it was the wheel, like no other prehistoric invention or discovery, what made mankind to rise from its primitive stage. I’ve always believed that even if the wheel was fundamental in the development of mankind, man first had to build tools to make wheels out of something; otherwise they would have been just a good theoretical conception.
But even despite the fact that building tools was in itself a pretty damn good start, I strongly believe that mankind’s first groundbreaking invention were knots. For even a wheel was a bit useless until it was tied to something. From my perspective, the invention of the wheel was an event bound to happen since there are many round shaped things in nature: from the sun and the moon to some fruits and our own eyes. Achieving the mental maturity of taking a string (or a resembling equivalent of those days) and tie it, whether around itself or to something, was, in my opinion, the moment in which the opposable thumbs of mankind realized they could transform it’s surroundings. Furthermore, at that stage the mental maturity achieved made it possible for man to remember how to do it over again in a consistent way.
The book ’2001 – a space odissey’ by A. C. Clarke, describes this process in the first chapter when a group of hominids bumps into the famous monolith. Their leader (i think his name was moonlight), under the spell of this strangely straight and flat thing takes two pieces of grass and ties them together without knowing or understanding what he is doing. I was pleased to read that I was not alone in that thought.
The concept of a knot keeps on amazing me given their variety and the different purposes they serve according to their properties. These were known to ancient sailors who have elevated the task of knot-making to a practical art form. The mathematical background behind them has served to lay one of today’s most fundamental (and controversial) theories about the composition of matter: string theory. Next time when you make the knot of your necktie think about this tedious, obnoxious little habit was based on something groundbreaking that truly makes us stand out from the rest of the species in the animal kingdom.
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.
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).
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.
