LEARN #1 – week 115 of my PhD

Good Morning world! Here is the first edition of LEARN, your favourite  weekly blog series from now on! This is the recap of what I have learnt last week:

Psychedelic image of the Hough Transform for a sine wave

Monday: Hough transform – Despite being extremely surprised that on a Monday I was motivated enough to learn new things, the hough transform was extremely fun to learn. It has a very simple math that allows you to extract linear features of an image. I needed that for extracting some information on sine waves in my pictures. Although for my problem I would need to define my own transform for sine waves decompositions, the simple application of the simple hough transform creates damn-good-looking images!

From left: kymograph of a measurement I am doing (no spoilers for now); extraction of maximum intensities position; fitting of results with various sine wave functions.

Tuesday: I learn that I could spend a week implementing my hough transform, or using the properties of my image to do a simpler analysis in just one afternoon (thanks to the suggestions of a clever friend of mine).

Typical Scottish Chick

Wednesday: Some of my experiments involve chicken embryos, during development. In total, from fertilisation to hatch it takes 20-21 days. In my study, though, I am looking just at the first 2 stages, during the first 6-7h of the embryo. In particular I am interested in the transition between stage 1, when the embryo is formed just from the area pellucida (a thin layer of epithelial cells) and a collar all around called area opace, and stage 2, when it start to develop what is called the primitive streak. What I learn on Wednesday is that the feature that appears in this transition, Koller’s Sickle, last just 30 min (at most). So this would be the timeframe of my experiments!

Ant-Man and his scary army

Thursday: After a disturbing intro about Lotus Birth, and still pondering about chick embryos development, another one of my clever friend pointed out how convenient would it be for humans to develop in elastic eggs. His argument was based on the fact that the humans’ head size is limited by the way we deliver our offspring. In fact, we have merely a brain:body ratio of 1:50, while small ants would go up to 1:7. One could argue that the number of neurons in ants is more than 300000 times smaller than humans, but I would reply by warning them about the secret plan ants must have. In fact, while one might think the humans are the highest source of change on planet earth, they move just about 35 billion tons of earth every year against the about 50 billion ants move around the globe*. And since ants have a very strong social intelligence, it is reasonable to ask “Why are they moving all this stuff?”, “How are they organising it?”, “Are they aiming to rule Earth?” and more importantly “Why isn’t Antman the most powerful superhero of all?”

PCA of a fish

Friday: Finally, just before to head to the pubs for drink, another clever friend of mine (that unfortunately does not have a blog to link to) explained me about Principal Component Analysis. I found it extremely clever, and I suggest you to check this interactive explanation! (It’s 01.21 am- I am quite tired, and still need to shower and I also hope to get some sleep before working: sorry if I don’t explain it myself)

See you all next week! In the meantime, don’t forget to LEARN Every day A Remarkable Notion! ūüėČ

*  This is calculated assuming that ants move 25 metric tons of soil per ha every year. This number is obtained by averaging the only scientific data I found online (64 tons for the P. Badius Ant, 1 ton for very small ants as the Trachymyrmex septentrionalis30 tons as reported here for non specified ants, 10 tons as reported for Australia for generic ants).
The average is not weighed, and I felt satisfied with it just because it turned out to be more conservative than 50 metric tons per year, the most commonly reported number on the subject (but of which I was not able to find the source).
The calculated amount of tons is then multiplied by the surface area of earth that is inhabited by ants (pretty much everywhere except Antartica).


No, I am not giving you an order neither a suggestion.. ok, it can be seen a little bit as a suggestion, to be fair. More than that, LEARN is something I have been doing (or trying to do) in my PhD.

‘Yeah, like ¬†everyone else doing a PhD’ – You might think!

Not quite so, and not because I am different from everyone else, but just because I don’t literally mean it in as in “learn”, the verb. Not just.

LEARN is a project and it contains anything I believe in on the way to become a better person (yes, a better person, not a better scientist). It is an acronym for “LEARN Every day A Remarkable Notion”.

I am night shower person, but instead of having brilliant ideas and admirable moments of clarity about life, the universe and everything, I spent my reflection time drawing conclusions about the past day. And it can gets very depressing. It often feels like my days are passing with me doing nothing, or nothing that matters at least. As if I completely wasted my time. And time, and jelly beans, are the most important thing we have. At the beginning of the year, I argued that it is just a matter of looking at things from far away to appreciate the big picture. Now I am taking a little step further: I want to give importance to the small things. I decided that in my PhD, or what is left of it, I would learn one thing everyday. Sometime it is something really important for the project, some others times it is something it would turn useful just for personal growth, and often it would be some weird curiosity one of my peers informed me during lunch time.

I have the power to make valuable all the time I spend doing this job, and if I learn something everyday, I will be a better person. From the small and funny things to the big ones. I will be posting them weekly, for everyone to learn something new and/or just help you focus on what you have learnt that day, that you never consider important.

Why am I so proud of it that I want to share it with the world?

  1. It is my first recursive acronym, and I love recursive acronyms – you have been acronymincepted! Welcome.
  2. It makes me feel good with myself and help to put things in perspective and highlights the positive achievements, even the ones that looks so minor!
  3. It is easy for blogging, and hopefully, it will help me to blog more.

So, stay tuned for a weekly update of LEARN!

Let’s kick the Quantum Beat

As a newbie in the field of biophysics, I had to take some course in biology. In my case the course, luckily, was addressed to physicists, and one of the suggested reading was Schroedinger’s “What is life?”. I did not know that Schroedinger wrote about this topic and, of course, I was curious and puzzled. I wanted to read it, and if you want to find a book nowadays, you usually type amazon.com and look for it. The problem with this approach is that Amazon, though really helpful, is sneaky and starts this evil suggestions thing in which I usually get trapped. This time the trap was more than well placed. Among the suggested readings, there was this:¬†Life on the Edge: the Coming of Age of Quantum Biology.¬†

Now, if there is something you need to know about me is that the mere word Quantum must trigger something in my mind and you immediately have my fully devoted attention.

“I would like to have 200 gr of brown bread, please.”

“Classic or Quantum?”


“Would you like to have the Classic brown bread¬†or the Quantum one, then?”

“Give me 5 kg of the quantum one!”

And it may works to let me buy things. So my mind turned blank about Schroedinger’s one (now in my wishlist) and I bought Life on the Edge instead.

Continue reading “Let’s kick the Quantum Beat”

New Resolution(s)

New year resolutions is not really my thing. But in the last year I did so many things that are not my things, that I can actually try this one as well.

But first, what about a quick recap of the last year?

It all started, like any other year does, at 00:00:01 of the 1st of January. For me the first second of 2015 had place on an overcrowded Princes Street in Edinburgh for what is known to be one of the best New Year Eve party in Europe, which -just to confuse tourists- is called Hogmanay instead of New Year Eve party. The end of the party, involving hugs from strangers, double fireworks show, R. Burns sonnet singing, signed the end of the holiday season and the start of one of the toughest year I have experienced since puberty.

For the first time in my life, I had to¬†really¬†ask myself “What am I doing with my life?”

Is this what I want? Am I happy?

Now, if I was a philosopher, those would have been just some simple mind exercises, but I am researcher, which makes those questions much more insidious.  The past year, I had to deal with overload stress, with failures, with missed achievements, with delayed deadlines. All things that РI am sure Рany researcher is used to.. but for me, this was the first time to seriously deal with these issues. And the worst was the feeling that I was not having fun any more doing my job.

The smartest of you may have noticed that I used the past. Yes, things have changed. Many things have helped, and surprisingly none of them is related to getting results.

The most helpful things have been knowing that I am not alone. Other researchers in the same program I am were sharing the same feelings, and that helped me to realise that it may have been a phase I needed to pass.  Some useful readings are about depression and stress in academia and about the imposter syndrome.

But the most important thing that has changed my¬†mood¬†is the understanding that I am not who I am because of the job I am doing. I have always pictured myself as an academic, but what if I will be not? This option was terrifying for me, feeling like I could disappoint the expectations of everyone I know. The moment I figure out that my life is plenty of many other things, everything started to get in the right perspective. I have awesome old date friends, and I have made new gorgeous friends thanks to this PhD project. Trying to rediscover¬†who I am, I dusted some of my hobbies, like drawing and painting. I went sailing. I took off as many weekends I could to meet friends and travel around a bit. My partner and I started to live together, bought a house and we’ll get married.

And guess what? I started to have fun again! Being released by the pressure of disappointing others and the nightmare of failure, I was free again to spend afternoons in the lab with a free mind. And it was fun! It is fun! After this epiphany, it was easy to go back and start to appreciate the achievements I have done and the things this phd offered me so far, like a period abroad for a collaboration (meeting awesome people!), a very long list of acquired skills from chemistry to cell culture, from computing to engineering, out reach opportunities to share science enthusiasm.

At December 31st of 2015, I still don’t have a publication ready to go, I still have to collect data and I am sure there are so many more experiments that will fail. But now all of this is part of the fun.

cropped-blogMy 2015 felt like staring at 8-bit picture from too close. You can see the single pixels, but you cannot pick the whole figure. 

But by the end of the year, I was able to step back and to understand those strange square confusing scaring unclear shapes for what they are. Pixels in a bigger frame, where the picture is loading. Sometime the download speed goes back to the old-day 56k, but sooner or later you can grab the whole thing.

Now that I have everything, 8-bit starts to look a bit out of focus for my taste. This is why, for this year, instead of an extensive list of my good intentions I have just one big goal:

a new better resolution!