Category Archives: Scandal

No, seriously, why can’t orbitals be observed?


The concept of electronic orbital has become such a useful and engraved tool in understanding chemical structure and reactivity that it has almost become one of those things whose original meaning has been lost and replaced for a utilitarian concept, one which is not bad in itself but that may lead to some wrong conclusions when certain fundamental facts are overlooked.

Last week a wrote -what I thought was- a humorous post on this topic because a couple of weeks ago a viewpoint in JPC-A was published by Pham and Gordon on the possibility of observing molecular orbitals through microscopy methods, which elicited a ‘seriously? again?‘ reaction from me, since I distinctly remember the Nature article by Zuo from the year 2000 when I just had entered graduate school. The article is titled “direct observation of d-orbital holes.” We discussed this paper in class and the discussion it prompted was very interesting at various levels: for starters, the allegedly observed d-orbital was strikingly similar to a dz2, which we had learned in class (thanks, prof. Carlos Amador!) that is actually a linear combination of d(z2-x2) and d(z2-y2) orbitals, a mathematical -lets say- trick to conform to spectroscopic observations.

Pham and Gordon are pretty clear in their first paragraph: “The wave function amplitude Ψ*Ψ is interpreted as the probability density. All observable atomic or molecular properties are determined by the probability and a corresponding quantum mechanical operator, not by the wave function itself. Wave functions, even exact wave functions, are not observables.” There is even another problem, about which I wrote a post long time ago: orbitals are non-unique, this means that I could get a set of orbitals by solving the Schrödinger equation for any given molecule and then perform a unit transformation on them (such as renormalizing them, re-orthonormalizing them to get a localized version, or even hybridizing them) and the electronic density derived from them would be the same! In quantum mechanical terms this means that the probability density associated with the wave function internal product, Ψ*Ψ, is not changed upon unit transformations; why then would a specific version be “observed” under a microscope? As Pham and Gordon state more eloquently it has to do with the Density of States (DOS) rather than with the orbitals. Furthermore, an orbital, or more precisely a spinorbital, is conveniently (in math terms) separated into a radial, an angular and a spin component R(r)Ylm(θ,φ)σ(α,β) with the angular part given by the spherical harmonic functions Ylm(θ,φ), which in turn -when plotted in spherical coordinates- create the famous lobes we all chemists know and love. Zuo’s observation claim was based on the resemblance of the observed density to the angular part of an atomic orbital. Another thing, orbitals have phases, no experimental observation claims to have resolved those.

Now, I may be entering a dangerous comparison but, can you observe a 2? If you say you just did, well, that “2” is just a symbol used to represent a quantity: two, the cardinality of a set containing two elements. You might as well depict such quantity as “II” or “⋅⋅” but still cannot observe “a two”. (If any mathematician is reading this, please, be gentle.) I know a number and a function are different, sorry if I’m just rambling here and overextending a metaphor.

Pretending to having observed an orbital through direct experimental methods is to neglect the Born interpretation of the wave function, Heisenberg’s uncertainty principle and even Schrödinger’s cat! (I know, I know, Schrödinger came up with this gedankenexperiment in order to refute the Copenhagen interpretation of quantum mechanics, but it seems like after all the cat is still not out of the box!)

So, the take home message from the viewpoint in JPC is that molecular properties are defined by the expected values of a given wave function for a specific quantum mechanical operator of the property under investigation and not from the wave function itself. Wave functions are not observables and although some imaging techniques seem to accomplish a formidable task the physical impossibility hints to a misinterpretation of facts.

I think I’ll write more about this in a future post but for now, my take home message is to keep in mind that orbitals are wave functions and therefore are not more observable (as in imaging) than a partition function is in statistical mechanics.

Women in #CompChem and the rest of STEM


In the past I’ve avoided this topic for various reasons. First, because I strongly believe that focusing on labels perpetuates them, and as scientists, we should always rise above them, for is science and not scientists what’s important. I remember my former PhD advisor, Prof. Cogordan, saying that “Liberties are exercised, not demanded“. Take Rosa Parks, for instance, her refusal to move to the back of the bus was an exercise of her liberty, and one that moved to a profound change, alas not without turmoil. But should I really call it a label? since it applies to roughly half the potential brain power available in the planet it then becomes a relevant question. Are equality and political correctness mutually exclusive terms?

It could be argued that I talk from a privileged position being a male scientist but since I’m a Mexican, non-white, non-US-based, male scientist those privileges are only so many.

I first began drafting this post way back before November 2016, when the misogyny displayed by a presidential candidate was in everyone’s mind to such a large extent that even when it even seemed prone to cause his demise it didn’t. The women’s march in D.C. has proven the topic to be still quite relevant though, and next April 22nd, Earth Day, a scientists march will take place to protest against policies that put science -and therefore mankind- in jeopardy. Some particular issues associated with the march will be the communication gag orders against scientific federal agencies; the consequences of the travel-ban to scientists from black-listed countries and, of course, the threat of having a misogynistic environment on the status of women in STEM careers.

Fact: There is a clear selection bias since there is still a large number disparity between men and women in academia throughout the world and since the number of academic position is growing at a much lower rate than the number of scientists competing for such positions, the race has become tighter and usually women take the worst part of the deal. There is a leaking pipeline in which women don’t reach the end of the race. I imagine in some cases it may have to do with maternity as it is still conservatively perceived by most countries but issues like harassment and condescension are not to be ignored.
Fact: Scientific curiosity is innate to all human beings -which confirms the above mentioned bias- therefore talking about encouraging young women to pursuit a career in STEM is plain stupid; they don’t need to be encouraged they must stop being discouraged somewhere along the path. The playing field for both genders should be leveled or science risks loosing half the population in these dire times in which all the brain power available is much needed. Also, I fear the continuous talk about these disadvantages could be off-putting for future generations of women who might be interested in undertaking STEM careers. Leveling the field for female and male scientists should be done and not just demanded but details about the mechanisms to accomplish it are still unclear and vary from one institution to another. Here in Mexico, for instance, all public universities have collective contracts, therefore every scientist in a given level earns as much as another in the same level. In other countries salaries are personally negotiated and therefore each scientists earnings vary, which has led to women earning less on average. Now, the ease with which levels are climbed within an institution are also a matter for debate. Does this mean that earnings and positions are the main problems women face in academia? Could they be the best starting points? Is the rate of enrollment the root of the problem? If so, are us teachers and professors to blame?

Another reason why I avoided this topic was because it would seem so patronizing on my part to give a shout-out to women whose work in computational chemistry I so much admire when I myself could only aspire to one day have work of their quality. They definitely don’t need my praises because they have well earned all our admiration. Nonetheless, here is a link to a great directory of women working in computational chemistry in which some great names are found such as Anna Krylov, Gloria Tabacchi, Romelia Salomón, Patricia Hunt, and so many more great scientists from all over the world. Here in Mexico we count with names such as Margarita Bernal, Patrizia Calaminici, Annia Galano, Estela Mayoral and so many other. It is hard to make a comprehensive list, and as I said before I could only aspire to have work with the same quality as theirs. The importance of recognizing and promoting women to take a career in computational chemistry will in short be addressed by the FemEx-NL-2017 conference next June 22nd in the Netherlands; their motto is “Promoting female excellence in theoretical and computational chemistry”, certainly a worthy and noble endeavor for a problem far from solved.  

Perhaps another good reason for writing this post lies in the image below. It is a true statement but we should analyze the causality for it and fix whatever it is we’re doing wrong because it is certainly not the plumbing:

I have a daughter. I want her to be able to do whatever she wants when she grows up without deterrence from unfairness. I want a world for her without labels so she never has the option of playing ‘The Woman Card’. It wouldn’t be fair for anyone around her.

This wont be the last post on this topic. Please share your views in the comments and criticism section. They are all welcome.

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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, took place: 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 presented 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 charge for her writings, 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 nonetheless; but at the same time 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?

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