My take on preprints

I am sure you’ve heard the buzz about preprints in biology. Preprints have been a thing for a long time now in physics and math. The idea is that you submit your paper in a more or less finished form to a server called arXiv (pronounced archive), where their manuscript only undergoes very cursory approval but no formal peer review. It is then available for anyone to read and comment on. Biology took much longer to accept preprints, but the movement has been gaining momentum in recent years. There is a biological arXiv twin called biorXiv, and it has become very popular, especially among computational biologists.There are many advantages of preprints. First, you get to get your story out quicker and people can find out about it sooner. Continue reading

Grieving for failed ideas

As scientists we always come up with ideas – solutions to more or less well known problems in our areas of interest. The ideas may be applicable only to our specific project, or they may be general solutions to a much broader set of problems. The more specific the idea is to our area of expertise, the more likely it is to be feasible, but sometimes an outsider can see the problem from a completely new angle and come up with a novel solution that no-one had thought of before. That’s why it’s sometimes good to go out of your comfort zone and try to come up with solutions to problems that are a bit outside your immediate sub-field. The flip-side is that the solutions that you will come up with typically have a fundamental flaw that makes them unfeasible.

I have recently spend a couple of days trying to devise what I thought was an interesting strategy to address a relatively broad set of problems in molecular biology. Turns out, similar solutions had been tried and work only in a very limited set of circumstances. Continue reading

Hacking the microscope

You know those super-expensive accessories that research equipment manufacturers make you pay through the nose for? A while back I bought a pretty expensive Olympus microscope. Since my budget was limited and I really wanted a best-of-the-best objective lens and a state-of-the art camera, I had to find savings wherever I could.  For that reason I did not get a filter wheel/shutter hand switch, which is a must if you want to operate the scope without the software running. Having to launch the the cellSens software to switch fluorescence filters was so frustrating that I caved in and requested a quote for the switch. Believe it or not, but this plastic box with a couple of buttons costs almost $1000. Continue reading

Polish funding agency gets its own public grant database

Those of you familiar with the US National Institutes of Health are probably aware of the NIH RePORTER – a public database of grants funded by the NIH with an advanced search system. I was really impressed that the Polish national funding agency (NCN – Narodowe Centrum Nauki – National Science Centre) set up its own equivalent – the “projekty” database. Continue reading

FUGA is dead, long live SONATINA

The report of the most recent National Science Centre council meeting is up on the NCN website. The most interesting piece of info for me was some new details of the upcoming SONATINA call for proposals. The SONATINA grant replaces the now officially burried FUGA grant, which used to be addressed exclusively to “mobile” postdoctoral fellows, who changed institutions and voivodships and wanted to seek better career prospects away from the institution where they did their PhDs. This worked out great for my new postdoc Łukasz, who got one of the FUGA grants and was able to move from Łódź to Warsaw. The SONATINA is different in many ways, but in some ways also resembles the FUGA grant. Continue reading

Can we solve research misconduct?

Just the other day I was reading a Nature opinion piece on deliberate research misconduct: how it affects the reproducibility science, and what we can do about it. The authors proposed a number of solutions, but most of them focused on punishing the perpetrators. Punishments should be more severe, they argued, the PIs should be held accountable for their trainees’ misconduct, and institutions should be forced to give back money gained by research dishonesty. I’m not sure I agree with this solution. Continue reading

The geography of NCN grants

The principal Polish agency that funds basic research – the National Science Centre (Narodowe Centrum Nauki – NCN) recently published data on grant success rates and total awarded amounts divided by institutions and departments. I decided to play around with the data a little bit to see the geographical distribution of NCN largesse. The results are pretty striking: Continue reading

The gory details – experiment design guide for beginners

In the previous post I’ve outlined the strategy that will allow beginner scientists to understand the complexity of a research project – something that they often struggle with. From the “tree of life” view of the research project there is a rather straightforward path to understanding the significance and interpreting the results of each experiment that they perform. I recommend that each beginner scientist answers (ideally in writing) the following questions before they even touch a pipette:

  1. What is the goal of this experiment?
  2. What is the hypothesis?
  3. What is the approach?
  4. What are the experimental groups and controls?
  5. What are the expected results?

Continue reading

The big picture – project perception guide for beginner scientists

One of the things I have learned the hard way during my first year as group leader is how easy it is to overestimate the ability of beginner scientists – graduate students, interns, undergraduates – to grasp the “big picture” of the project. Beginners are usually quite good at performing experiments and processing results, but they typically find it very hard to visualize where the experiment fits in the grand scheme of their project. I would like to propose a framework that will make it easier for beginners and their mentors to stay on the same page when it comes to the big picture of their projects. Continue reading

Academaze – the awesome new book by Xykademiqz

The road of an academic scientist is long and tortuous. Many pitfalls await the hapless young researcher, so any advice is always a great bonus. I have been relying on Twitter and a bunch of great blogs (see my blogroll) to get my fix of do’s and don’ts in academia, and it has served me well – I now have the coveted group leader position at a major university in Poland and I use the blogroll as a constant source of information and support in my ivory tower woes. One of my favorite blogs has always been xykademiqz, written by a successful mid-career group leader in the physical sciences. The blog is filled with great advice and down-to-earth musings on the “human” side of research. That’s why I was really excited when I heard that xykademiqz is coming out with a book, which, as I understand, is a collection of her most successful blog entries organized in a way that will make for an interesting narrative. The book is here, and I got a glimpse of it as an early access reader. Let me tell you this – it is pure gold! Continue reading