Monthly Archives: September 2013

My take on GMO’s


September’s issue of Scientific American is all about food; food and food science, that is. In it, there are a couple of articles on Genetically Modified Organisms (GMO’s) and there is also this blog post in their website being in favor of GMO’s, and I for one, stand by them. There is a global science illiteracy problem going on which accounts for the fear and misinformation most people get on important issues and the fear against GMO’s is one of them and a particularly disturbing one since it deals with a primal necessity of mankind, one that cannot be disregard at any time: Food.

I think when lay people hear GMO immediately think of some sort of Frankenstein plant or some other horror movie monster. For some reason people think technology=good and food=good but food-through-technology=really-bad. Of course we should be weary of what we put on our tables but in order to be weary we first must be thoroughly informed. Us people in favor of controlled GMO technology tend to give these boring arguments on DNA and vectors and so on while the opponents gather more fans with the more alluring image of the Franken-corn! Let me use a real life example to start this discussion

Let me use a human example: My wife has an amazing health. She gets the flu once every year (if at all!); gets knocked down for a couple of days and that’s it! she is back on her feet working and partying the following 363 days of the year. I, on the other hand, am not that lucky. I’get congested very easily with changes in temperature, so every time we go swimming (twice a week, if at all) I end up sneezing my lungs out afterwards. My gastrointestinal system is also very faulty, I easily get… well, you get the picture. Whenever we have kids, it would be easy to presume that they will be not as healthy as their mother but not as sickly as their old man, but something rather in the middle. It could also be the case they were entirely like one of us in the health department, who knows! Lets say they are in the middle. We have now performed a genetic modification which improves my genetic traits. My hypothetical kid is now an improved version of myself but not so much of their mom’s, but definitely not a clone of neither! These hypothetical kids will be humans, just like their mom and I. The key in the above hypothetical procedure is the statistical variability in it. We should have many kids so around half of them had an intermediate health (assuming no genetic trait is more dominant than the other). With plants is the same thing: You might have some corn species with huge grains but low resistance to droughts while other species might need less water to fully grow although the product is not as good as the former. When combined, both species will yield, hopefully, an intermediate species which can be iteratively improved until we achieve corn with big grains and low water demands.

What we cannot do now, is to have these hypothetical kids reproduce with one of their parents as to yield an even healthier human! But when it comes to plants, such as corn or wheat, incest is not an issue. Pollinationcross pollination and plant grafting do exactly this by combining the traits of some species with another’s. Almost no food found in any market has not gone through this process through the last couple hundred years. But this Higher Power (I mean of course farmers and botanists) that has yield this delicious and nutritious vegetables available to us, have worked on a trial and error fashion. Nowadays we can be more precise on what traits we want our vegetables to have from one generation to the next by using genetic engineering techniques. With GMO’s we can create more food resources with a lower energy investment, a key issue in sustainable development of any nation; we can also address some nutrition deficiencies just like it was done in The Phillipines where beta-carotene (the yellow pigment in oranges and carrots) was introduced into rice in order to attack a Vitamin-A deficiency in kids that was rendering them blind.

Europe doesn’t allow the sale of any processed food containing GMO’s while in the US almost no processed food doesn’t include, at any level of their production, a GMO ingredient, but the reason behind this is because in Europe the debate ended before it began while in the US there is still debate on whether to add a label specifying the presence of GMO’s on every food product. The inclusion of such label, at this stage, would only add up to people’s fear of GMO’s because it would be perceived as a ‘warning‘ instead of just as ‘information‘.  Scientific literacy is urgent not just so a good decision is taken but to start the debate! At this point the only thing keeping those labels away from supermarket products is the billions of dollars in lobbying by big companies such as Monsanto (which is not the devil, please put away your crucifixes) and DuPont. But the issue shouldn’t be about money, it should be about the way scientific reasoning should steer the decision making process in this and any other controversial issue.

The potential benefits of GMO are central to the sustainable life and development of our nations, so instead of fearing them lets understand them first.

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How to read (and perhaps even write) a scientific paper


This post was inspired by this other one, featured in WordPress’ Freshly Pressed section, on how should non-scientist read a scientific paper.  While the approach presented therein is both valid and valuable, I’d like to address the way I think a scientist should read a paper, given the fact that we need to read a lot of them at all times. Each scientist has their own reading style, not to mention their own writing style, and while my CV could indicate I don’t know how to do neither one, here I present to you my scientific-paper-reading style which I consider to be the most suitable for me.

I’d like to start by emphasizing that I dive into scientific literature in a bona fide fashion. That is not to say I’m totally naive or even gullible, but even when science is all about questioning and casting doubt onto all sorts of claims, we can’t re-develop every bit of science we need. At a certain point we must start *gasp* believing trusting other scientists’ claims. Reading in what I call bona fide is not mutually exclusive with critical reading. This sort of scientific trust is earned, to a degree, mostly by two indicators: Author’s preceding reputation at the time of publication of any given paper as well as the journal’s. Both indicators aren’t without controversy and flaw.

The way I read a paper is the following: I start with the Abstract, then follow with the Conclusions, then the Results section, sometimes I read the details of the methodology and seldom read the Introduction. Let me explain.

I read the abstract first because I read in bona fide as I hope the authors wrote the paper in bona fide. If properly written, the abstract should include all the relevant information as to what was done, why, and how but also point to the knowledge derived from it all: Their conclusions! and that is why I follow with that section. I’m interested in knowing what the authors learned and ultimately want me to learn about their study. Once again I’m reading in bona fide, so I hope they weren’t tempering their results to fit their preconceptions, that all experiments were thoroughly self-judged, validated, correlated, referenced and controlled. Recently, my sister Janet, who is a physicist working on her PhD in neuroscience, told me about some friends of hers who never (shall I say, never have I ever?) read the conclusions as to not becoming biased by the authors. To me it seems like too much work having to scrutinize every piece of data again in order to come up with my own conclusions when authors, collaborators, people on the hallway down the lab (optional), referees and editors (vide infra) have already (hopefully) done it (properly). Still I put on my scientist badge and question everything I critically read in the results section trying thus to understand how did the authors reached their conclusions and asking myself if I could come up with something entirely different. No? OK, how about something slightly different? Still no? Well, do I agree with the authors on their findings and their observed results? And so on. I like thinking that my critical reading process resembles the Self Consistent Field method which iteratively reaches the best wavefunction for a set of certain given conditions, but it never reaches the exact one.

The methodology section is a bit tricky, specially when it comes to computational chemistry. Back when I was a grad student, working in an inorganic chemistry lab, I’d only read the methodology if I had any plans of reproducing the experiment, other than that I didn’t care too much if reagents were purchased from Aldrich or Fluka or if the spectrophotometer was a Perkin Elmer one, I just expected authors to have purified their reagents prior to usage and calibrated all spectrophotometers. Now in computational chemistry I read about the methods employed, which functional and what basis set were used and why were they selected are my most frequent questions, but the level of theory is usually stated in the abstract. I also take a look at what methods were used to calculate which properties; these questions are important when we have to validate our trust in the results in front of us.

Finally, I seldom read the introduction because, if the paper is relevant to my own research, I don’t need to read why is important or interesting, I’m already sold on that premise! that is why I’m reading the paper in the first place! If both me and the author act in bona fide, we both already know what the state of the art is, so lets move on because I have a ton of other papers to read. Hence, I read the introduction only when I’m trying to immerse myself in a new field or when reading something that seems interesting but which has little to do with my area of expertise. There is another reason why I almost never read introductions and that is that, even when I try to work in bona fide, there are a lot of people out there who don’t. Twice have I received the reviews from a mysterious referee who believes it would serve the work a great deal to cite two, maybe three, other papers which he or she lists for your convenience, only to find out that they all belong to the same author in each case and that they are not quite entirely related to the manuscript.

In the title of this post I also try to address the writing of a scientific paper, although I’m not an authority on it, I think today’s key phrase is bona fide. So to young and not so young scientists out there I’d ask you to write in bona fide, please. Be concise. Be convincing. Be thorough and be critical. This is science we are doing, not stamp collecting. It shouldn’t be about getting all sorts of things out there, it is about expanding the knowledge of the human race one paper at a time. But we are humans; therefore we are flawed. More and more cases of scientific misconduct are found throughout the literature and nowadays, with the speed of blogging and tweeting, we can point at too many of them. The role of bloggers in pointing this frauds, of which I’ve written before here, is the subject of recent controversy and possibly the topic of a future post. We are all being scrutinized in our work but that shouldn’t be an excuse to make up data, tinker or temper with it, to push our own personal agendas or to gain prestige in an otherwise wild academic environment.

I for one may never publish in Science or Nature; I may never be selected for any important prize, but even the promise of achieving any of those is not worth the guilt trip of lying to an entire academic society. I try then, to always remember that science is not about getting the best answers, but about posing the right questions.

What is your own style for reading papers? Any criticism to my style? How different is the style of a grad student from that of a researcher?

As usual thanks for reading, rating and commenting!

More interns!


I’ve been neglecting this blog a lot lately! It would seem as little or nothing is going on in our lab but it’s quite the opposite, a lot of good stuff is going on and most of the excitement comes from the results obtained by a few more interns.

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Eduardo Cruz

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Alberto Olmedo

Alberto and Eduardo came just as the previous group of interns left. They’re both undergrad students in Pharmaceutical Sciences at Universidad de la Cañada in southern Mexico. My good friend, Dr. María del Carmen Hernández, referred them to me to do a stay during their summer vacations. They are taking where the previous interns (Paulina, Eliana, Javier and Daniel) left and have now obtained the interaction energies for five different host-guest aducts for 3-phenyl-1H-[1]bezofuro[3,2-x]pyrazole, a tyrosine III kinase inhibitor, currently under research for the treatment of leukemia, better known to us as GTP. As before, our molecular carriers are a wide selection of functionalized-calix[n]arenes. These calculations turned out to be rather lengthy; they were all performed at the B97D/6-31+G(d,p) level of theory in order to account for dispersion forces in pi-pi interactions between the aromatic rings in both species.

The third recent addition to our lab is Monserrat Enriquez, who is a PhD student under the supervision of my good friend Dr. Eddie López-Honorato (if you haven’t checked his blog on nuclear energy and materials for nuclear reactions containment go now and follow it; encourage him to post more often!). Monserrat will be co-advised by me. Her project lies within the scope of molecular recognition, materials recovery and bioremediation; calculations and simulations will help the experimental team to point the synthesis of sequestrating agents in the right direction, or, at the very least, to have a better understanding of the forces and interactions lying beneath the formation of such complex structures.

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Monserrat Enriquez

Last but not least, Luis Enrique is back with a vengeance! He is determined to finish his study on other tyrosine kinase inhibitor drugs. Luis Enrique is an undergrad Chemistry student here in Toluca at the Autonomous Mexico State University, so he will come on his spare time and work from home every now and then; who knows! maybe he’ll end up with a dissertation by the time he finishes his undergrad studies!

But I’m to be left alone pretty soon, as Alberto and Eduardo will stay for a couple of weeks more and Luis Enrique will be here on his spare time. Monserrat will leave on Friday back to Saltillo in Northern Mexico to continue working on the experimental part of her research while working on her calculations from a distance.

Thanks to them for their invaluable help in the development of our research group, for their enthusiasm and hard work. You are now a part of this lab and its doors will always welcome you back!

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