Why do a phd?

Unfortunately my PhD is getting near to the end I know that the word unfortunately may sound strange for someone knowing how difficult it is to perform a PhD programme, but if you really enjoy it you will overcome every difficulty.

In this period of the year our lab is packed of post graduate students coming for interviews to get a PhD position and I had the chance to speak with some of them. They were asking me Why did you do a PhD? Do you like it? Is that stressful?

They really bring my mind back to 3 years ago

I reAnna Rita Liuzzimember that I took this decision with time. After my bachelor degree I only knew that I liked my subject Biology and Biomedical applications but I didn't have any idea on what to do in the future. Then I decided to continue with my Master degree and undertake an Erasmus Placement in the UK to enrich or s
tart my experience in research. At that time I was sharing my flat with five other PhD students and together with my new experience in the lab I started to have a rough idea of what it could be like to undertake a PhD programme I could see that they were not doing regular hours of work (not like a normal job), sometimes they were coming back home saying: it didn't work again! But they were really motivated and they loved science!

I think that the only driver in the whole journey is your self-motivation.

So what is your motivation? Is it the title of being a Doctor? Is it because your friend is doing a PhD as well or because you love your project and the idea of working on it?

If you are not convinced yet wait for a while and do not rush to it. After all this is going to be at least three years of your life and you need to make sure you will not run out of enthusiasm in the middle of the journey.

My good reason to do a PhD: if you like science and you want to be trained to be a researcher, if you want to find a research problem and figure out a scientific solution and you want to put in practise that solution. If you want to learn how to present your results and, in the end, put all your efforts in your thesis...then this is the best journey for you!

Anna Rita Liuzzi

The science of publishing

As this is an hot period for all the ESRs in terms of analyzing data, thesis writing, paper submissions, life decisions after the completion of their PhD, here I would like to tickle the young (but also the senior) scientists with a couple of articles I read and that kept me thinking about what I and we, as scientists, do every day to become and be part of today's scientific community.

Unpublishable negative results, reliability of results in peered review journals, unreproducible published experiments, statistical misapplication and low powered experiments make research in Pubmed a big challenge every day.

Silvia TarantinoI found the article "Trouble at the lab" from The Economist (October 2013) very interesting in pointing out some weak points in biomedical science today and sometimes even shocking for what it reported, like this passage:

"John Bohannon, a biologist at Harvard, recently submitted a pseudonymous paper on the effects of a chemical derived from lichen on cancer cells to 304 journals describing themselves as using peer review. An unusual move; but it was an unusual paper, concocted wholesale and stuffed with clangers in study design, analysis and interpretation of results. Receiving this dog's dinner from a fictitious researcher at a made up university, 157 of the journals accepted it for publication.

Dr Bohannon's sting was directed at the lower tier of academic journals. But in a classic 1998 study Fiona Godlee, editor of the prestigious British Medical Journal, sent an article containing eight deliberate mistakes in study design, analysis and interpretation to more than 200 of the BMJ's regular reviewers. Not one picked out all the mistakes. On average, they reported fewer than two; some did not spot any."

And few days ago, The Guardian has published "The games we play: A troubling dark side in academic publishing" where Dorothy Bishop, Professor of Developmental Neuropsychology at Oxford University and Fellow of the Royal Society lights on "questionable" editorial practices...I found it surprising and good starting point to think about what publishing can also mean nowadays.

Here I report some links:

Good reading!

It would be nice to hear opinions on the topic from the ESRs and as well from the PIs!

Silvia Tarantino

Bright side of the moon

In my previous blog I wrote about repetition of experiments. This time I want to show you that there is also a bright side on th

is process. Repetition of the same action may be annoying, frustrating or simply can drive us crazy. After multiple repeats of the same experiment, with attempts of modifying the protocol, we get stuck at a point where it still doesn't work.
Doubts appear, in our lab skills, knowledge and sometimes even in the sense of working in science. Then we enter into the next stage, in which we try to
find the cause of our failure. We start from the very beginning to understand where's the mistake or perhaps just a wrong comprehension. We dig again all the literature and technical support available in the subject, spend hours on finding what we missed at the first time. And here comes the nice and fun part of science (finally).Edyta Kawka

We find the solution!

Usually it is something simple, trivial that we considered as irrelevant. We adjust the protocol and fireworks! It finally works, we obtain nice results. There is a feeling after this long journey: relief, excitement, proud of solving the problem. We understand that it was worth to sacrifice time to get the answer.
And that is the bright side of this process the moment of solving the problem.

Edyta Kawka

Mycoplasma

Are your cells more sensitive to exogenous stress or are they just different? Decreased viability? Abnormal growth rate? Experiments not working as they should or used to? Strange results?

There are several causes, now I will write about the one that happened to me recently. It's called the Mycoplasma. Unfortunately contamination of cell cultures by Mycoplasma can't be visualized by light microscopy and morphological cellular changes can be unapparent. I had no idea why my cells are so sensitive until one of my colleagues told me about it.Andras detail

There are different ways to detect Mycoplasma. I used a special kit, which is a bit expensive, but faster then the PCR. If the cells are extremly valuable (whose cells are not precious right?) you can try to eradicate Mycoplasma with some special antibiotics (w
hich are very toxic and treatment takes time). I just simply got rid of everything, threw out the cells, medium.

So if you think that something is wrong with your cells, but there is no obvious reason, think about this tricky bastard.

Andras Rudolf

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