All posts by Fabio

PhD student @ CRAG. Bioinformatician.

Starting back over again. Welcome back.

It’s been a while in deed. I had to take my time to fix things in a lot of sides of my scientific life, and to feel ready to get back to my blog activity. In a 4 years- long PhD project, the second year always takes a little crisis along. Nothing special, and nothing really uncommon in the complex and diverse postgraduate world. I had to make up my mind on a couple of things, restore my initial motivation and organise my activity to close the ongoing projects and go further till the end of my thesis. Luckily, and thanks to some very important people that are close to me, I am now taking the courage to make some things clear and try and overcome my limits. Continue reading Starting back over again. Welcome back.

Turn your smartphone in a microscope ocular.

If you’re up for some Sunday biological geekerys, you might enjoy this video introducing the iDu Optics’ LabCam microscope adapter, that will fit your iPhone into a microscope ocular to show the image on the screen. On my old blog ATCGeek, I wrote a couple of comments on the possible role smartphones might have in biological research, and described some Android apps for genome browsing, or that geeky idea to build a microscope with a smartphone and a couple of pieces of plexiglass. Despite the comment of many is that these devices won’t be of much help in wet and dry labs, we can affirm that they can still provide “a little help” in many situations, such as easying the visualization of a genome sequence when you cannot leave the bench, or just helping in a better and more comfortable visualization of a microscope sample, as in this case.

iDu Optics LabCam Microscope Adapter is mostly designed to work for iPhone, even if a Samsung S6 version is available. You can buy it on the website  via PayPal, or on Amazon, but the price is still someway prohibitive. All the models range around 250$. Ok, you might want not to go blind each time you have to view something on a microscope, but maybe this is not worthwile this price, that is the only read drawback I get to see in this amazing product.

The evolutionary level of human violence — Why Evolution Is True

 

There’s a new paper in Nature about the level of intraspecific violence in humans and other species, written by José Maria Gómez et al. (free reference and download below). The question is how often members of single species kill each other in the wild, and whether humans are outliers. It’s already gotten a lot of attention in the press, […]

via The evolutionary level of human violence — Why Evolution Is True

GMOs, flatmates and lateral gene transfer.

Right about one year ago, I was sharing a flat with some Spanish guys in the deep heart of Grácia, an historical neighbourhood in Barcelona. To be honest, those guys fitted quite well into the definition of “friki” – Spanish transliteration of the term “freaky” – that indicate that kind of people attracted by oriental spirituality, organic food, ecological behaviours, flea market handmade clothes and hemp derivatives of all kinds. Boldly and briefly: hippies. Being an ecologist activist with radical autonomist positions (I am a bit hippie too), I tend to have a good relationship with this kind of people, at least till the moment when they understand that I am working in Science, in Biology, and most importantly in Plant Biology. The path from me explaining my work, and they asking about GMOs is very short, and my efforts to explain that I just study the evolution of plants without modifying them are normally useless. And right about one year ago, I had to spend a whole afternoon defending my work, and debunking a lot of misconceptions of them. Continue reading GMOs, flatmates and lateral gene transfer.

Welcome to the bioinformatics blog you are not looking for.

When I created atcgeek.net, I was a master student in cell biology and bioinformatics looking for a PhD position or, to better say it, I was a 20-something-almost-30 random guy who was looking for his way in science. And in life. At the time, I was working on a computational genomics project for my thesis, and was in the serious need to improve both my English, both my bioinformatics knowledge. I then thought that there was no better idea than to open a blog in English, and start writing about computational biology, evolution, complex systems, and other things that I used to ignore. In a language that I barely spoke. Sometimes a stupid idea might work, and writing on atcgeek turned out as a truly fulfilling experience. I had the opportunity to explore new fields, learn new things, practice and improve my English (to some extent), and discuss with amazing people. Later on, I finally got a PhD position in Barcelona, where I moved from Rome at the beginning of 2015. The impact with a PhD project was tough. I started to work hard to fetch my first results, and soon I realized that I had no much time to keep the blog updated. Also, I joined the Italian community of Barcelona, and started a political project with some new friends I met, that is now proudly known as the Barnaut Collective, and devoted to do independent information about Barcelona and the Catalan Countries in Italian and (soon) other foreign languages.

Anyways, and under many points of view, things were not so drastically changed. The almost-30 guy became a 30-something guy, with a PhD thesis to carry on, but stoññ many things to learn and fuzzy English to improve. I started to think for a way to back to blog, and concluded that despite I was not done with writing yet, the atcgeek project was gone. I needed a faster, cheaper and more effective way to communicate my thoughts. The best option was to back to wordpress.com and open up a lighter blog, with a major focus on the content, and the mere target to discuss about computational biology with the readers. The time for PunkBiology had come. A simple bioinformatics blog that you were probably not looking for, but where some good discussions and funny post may show up from time to time. During the next weeks, I will try to recover my atcgeek posts, and start to write some new ones. As for now, welcome back to my posts, and welcome to PunkBiology.

Oh, right. Why punk biology? Well, I guess I will find some time to put down a couple of lines to explain why I am quite sure that bioinformatics is the “punk side of biology”.

Those viral Evolutionary Biology notes. A late confession.

Time for late confessions. This story dates back to the 2000s, and it is about free diffusion of knowledge, internet, evolution, an angry academic and a monster (I mean “another monster”, distinct from the angry academic). It was the 2007, and I was hardly trying to find a way out from my bachelor degree. At the time, I had to do the exam of Evolutionary Zoology, which classes were held by Professor Raffaele Scopelliti at the Dept. of Zoology of the Sapienza University. I was never the one for sitting in a classroom, and skipped as much classes as I could. It was permitted, and the schedule was so terribly organised that was really hard to embed your commitments. This was the life at the Italian university during the 2000s. Courses overlapped, the thesis lab-work could take all your day, and the best you could do to survive was to choose a comfortable library to sit down and study for extra-session exams. I was told that things turned slightly better in the last years, but then this confusion matched a lot with my natural “too cool for school” attitude, taking me far from lessons very often. During the spring of 2007 I had few time to study Evolutionary Zoology, I did not attend the course, and needed a solution. Usually, the solution in these cases was to grab someone else’s notes, and one day my friend Amro showed up with a copybook full of notes from the Prof. Scopelliti’s lessons. The notes belonged to a girl I never knew the name. Amro had to return the notebook to her soon, and suggested me to photocopy all the pages.

I started to rewrite the notes on Google Docs, organising them as a real text book, with chapters, sections, headings and all the rest. It was tough sometimes, since the photocopies of a handwritten text are hard to read, and often it turned to be a matter of free interpretation. Also, from time to time I found my activity quite boring, and since I am a huge fucker, I started to thread jokes and foul language in my writing. As said, it was the 2007, and that story of the Flying Spaghetti monster was just starting to spread in Europe. As I started to rewrite the lesson that swiftly (and of course critically) described the alternative evolutionary theories, from Lamarck to Creationism, I had the brilliant idea to insert a description of the Flying Spaghetti Monster theory, taking care to mention that was a hilarious fact.

The exam day had come, and the result was strikingly good: 30 out of 30, the best mark you can get in the wierd Italian evaluation scale. The real problems arose later. I was very active in promoting things such as open science and the free distribution of knowledge at the time, and the best I could do in my own little was to publish my notes on a biology students unofficial forum we had (there was no Facebook yet, oldie me). The response was good. Students appreciated the initiative, the link was diffusing very quickly, and people was quite happy to read notes where some joke could eventually pop up from time to time and kill the bore. Unfortunately, a couple of months later, I spotted a post on the message board of the official website of the Faculty of Biology. It was authored by Raffaele Scopelliti, and the title was “Warning on Evolutionary Zoology fake-notes“.

I opened the message and the body was imperative and threatening. I don’t remember the exact words, but it sounded like this:

Dear Students, someone has published some very inaccurate and awkwardly incorrect Evolutionary Zoology notes that are referred to my lessons. I gave no permission to publish them. I urge you to quit studying from them. I don’t know the author of this brilliant work, but I swear that I will find this guy.

I gave it no much importance. My exam was done and registered, and I was far and safe from professor’s anger. But later on, I was explained how he came across my notes. First, some transcription errors spread out, becoming very popular among the students, just like the Haeckel’s Biogenetic Law that was written as “Haeckel’s Progenetic Law” because of a misreading of mine. Also, it seemed that anyone really liked the story of the Flying Spaghetti Monster to the point that many people reported it during the exam. In Italy the most of the exams consist in oral interviews, and those present told me that professor Scopelliti, after having heard the story of the monster for the umpteenth time, literally started to yell “who told you about this damned monster”?

The fact itself is funny, expecially if you consider the very formal italian academic environment. I admit that my story is of small interest, but I guess we could learn something from it. When I published online my document, I carefully and repeatedly warned the people that they had to check everything on it, that those pages represented just a raw product, and that it was full of inaccurancies to be corrected. Actually, this story taught me something on the way university students do their work. The most of the times people is so focused on learning as most notions they can, without giving the due consideration to the critical review. At the time, it made me think. I knew I wasn’t any better than the most of the people, and the same lack of criticism that gets students to talk about flying monsters in an Evolution exam could have affected me as well. Also, it was the first time when I experienced the danger of freely diffusing information on the internet, and some long reflections could be made on this point too.

But this is mostly a post for a late confession. Dear prof. Scopelliti, I have no idea whether you will ever read these lines or not, but I guess that you might remember this story. I just want you to know that it was me, that I am still trying to make my way in Evolutionary Biology, and no. I don’t apologise for what I did.

My notes were still better than the nothing you shared as course materials.

Choosing the right candidate. A lesson to be learned.

Being in science is basically a matter of applying for a position. As you graduate in your master, you swiftly approach your first “application round” for a PhD, and after your PhD, the endless post-doc route will take you into several cover letter writing, interviews and candidate selections. As an high level scientist commented to me once, after that his institute rejected (quite harshly I’d say) my application, it is fundamental to be able to properly attend an interview, because scientific institutions are importing the recruitment practices from companies. But how much are they effective?

In this TED talk, Regina Hartley, New York born Senior Professional in Human Resources (SPHR) from the HRCI, explains us that the right candidate may not be the perfect one. As you screen your candidates profile, one of the things that should matter is how much the person you are analysing demonstrated the capability to sneak out from hard conditions. Thus, an honour graduate in a prestigious university may not be as effective as someone who came out from a public university and had to face several difficulties in his/her life.

Here’s the link to the video in case player above does not work (I am having problems with that, actually).