What makes a GOOD mentor?

Nature has an interesting five-minutes in their latest podcast, on what makes a good mentor for young student, either at the PhD level or below (ehr, that would be me).

If I were to score my own mentor, I’d probably conclude that, with the exception of the last one, all of my official mentors did fail in one field or another. Still, I am not going to blame my own lack of success on them. It is, definitely, almost completely my fault. After all, they’ve worked hard to get where they are and it’s up to me now to show my muscles. Outside of the gym, though.

Still, the single most important thing I need from a mentor is bouncing ideas back and forth, and a safe weekly (or fortnighly, or monthly) meeting to make myself accountable for what I have done in the intervening time. I know it’s like admitting that I do not know how to prioritise my time and don’t put the right importance to the various parts of my life but ehy, isn’t this the reason while I am writing a blog post which will most likely be read by no-one?

So, in conclusion, I think I better press the goddamn button and start reading the paper. And not come back after five minutes to check how many hits I got. It’s not that I am lazy, more that I am easily distracted. Gawrsh!

The importance of good data

Data is everything.

Without data, my models do not take off.

Whether you work with proteins structures, experimental results, or God-knows-what, the quality of your work is influenced by the quality of the upstream data, and the trust you put into them.

Unfortunately, data are not so easy to get hold of. Good data are even more difficult to catch.

Very recently, at my work, I have discovered that a particular section of
my company does not like other people sniffing around their databases – they’re afraid that unskilled people may draw the wrong conclusions about their work – it is not simple science, we have been told, and please don’t demean it as such.

A little back in time, during my PhD, I discovered that you should not blindly trust data you’ve been handed over either: always check, and if possible, double check them. Confirmation of this has come during the previous months, when I spent a LOT of time cleaning up a database of experimental data from all the crap that found its way in there during thirty+ years.
I can tell you, it’s grueling. But in my line of work, I am told, data preparation is by far the most time-intensive activity one can pursue. Analysis of the results certainly takes less, and the actual model-building is a doodle.

Let’s take a (real-life) example: Experimental measures of pKa of a compound: how difficult can it be? Well, first of all, you must make sure that your data is actual experimental data – has it been measured? Not always: I was told that sometimes the compound wouldn’t bloody dissolve, so they would insert in the database the computed pKa, or the pKa of a similar compound(!).

Then, if you can get around this, there still is lot of room for errors, or at least weird uncertainties: in the case at hand, you get a handful of values for every molecule. How do you know which pKa corresponds to which atom? As it turns out, there’s a way of detecting whether it is a base or an acid – by repeating the experiment in water/alcohol mixtures, the pKa values do change, with acids’ values getting higher, and basis’ values decreasing – or the other way around, can’t bother to fact-check right now. So, in theory it is possible to say which is an acid and which is a basic pKa. Important, since a basic pKa will tell the pH at which your molecule becomes neutral (and below that, is positive) – an acidic pKa tells you when your molecules goes from neutral to negatively charged. Get them wrong, or worst mixed up, and your compound’s predicted properties (such as permeation of the gut walls and other membranes, but also retention in a chromatographic column) will go haywire.

But thats more or less it: now you know which one is basic and which one is acid. But how do you assign down to the very atom its own pKa? if they’re few, it’s easy. I mean, if you have an acid and a basic functionality in your molecule, the choice is trivial. If you have two acids, though, it’s all a matter of chemical knowledge, and intuition. You expect, from previous experience, some groups to ionize around certain pHs. However, the presence of charges and other substituents all around will greatly affect these numbers, and sometimes the ordering of them may even change. Big mess then – so how do you fix it? Well, some experimentalists use computer models to get a hunch, a suggestion on what may be going on. Which seems great, except when the reason why you’re looking at those data is exactly to validate those very same computer models. Then it sucks. Add to this the well known fact that most of these softwares do get it wrong quite often, and by a mile or two, and you’re left with a bemused expression…

Welcome to my frustrating world.

I have been freaking scooped :-(

I am a PostDoc. No, wait, haven’t defended the thesis yet, but am on my second year of PostDoc. One of my bosses (I happen to have many of them at every single stage of my carrer) defines me a PreDoc. I initially had a thesis writing block, then my (ex?) PhD supervisor caught the terrible thesis-correcting intestinal block.
Awful disease which causes him to pass me only one chapter of thesis per month, duly commented.
Gawk. To add on this, I felt it was rather pointless to start writing up the paper summarising my whole work, while corrections were not yet crystallised. A general statement about not wanting to re-write the same things twice, coupled with my indolence to actually sit up and write after work, when the bad belgian weather pushes me to eat lots of high-calories food and watch desperate Housewives and other corner stones of human knowledge. So, to make it short (ah!) I still haven’t published my work. And some months ago have come to know that someone else has published a similar one, although I am still ahead of them. What’s worst, these people don’t care to reference the previous PhD work that mine stemmed from. This pissed the hell out of one of my industrial supervisors, who’s a hell’s hound under the travesty of a nice guy – kind of cool, indeed. I wish I was cool and clever half of what he is. May be I’ll get there. Anyway, let’s not get out of track: they freaking scooped me. Actually, it did happen once already, during my first year, but back then I didn’t complain too much, the group who did it was much more powerful than me on my own, so quite frankly theiy did a much better job than I could have done myself, inexperienced as I was. But not this time. I usually think of me as a mediocre scientist, but people keep telling me that I sell myself too short. Mah… I just don’t feel like I’m getting close to the Nobel anytime soon, and certainly I lack the drive and the focus. Unlike many other colleagues, may be less smart, but certainly more devoted to their work. I am still the curious ten year old, tinkering and playing with cool things. And getting off track. Again.

I have been scooped. Not really, but some other people are using techniques very similar to what I have been developing. I better get my act together and write down that damn paper (or two) – And bang on my boss’ door to have back my final chapter. I’m pissed too. Thouroughly so. Royally so. Do not get close to me, oh sinner, for thou shall repente thy choices.