Did you really write that paper?

It happens sometimes that the job done by a single scientist get published with more than his name on it. He’s usually the first author, except in Italy and other third world countries, where some professors pretend them to be on top. He’s relegated to second place, unless the professor above has a favorite pupil who needs a push to get/stay into the tenure track.

Anyway, this post is not about unjust usurpation of authorship at the hand of elder academics. It is rather on the careless co-authorships practiced in some research groups, where all those belonging share authorships to any papers so as to augment their paper count in their CVs. Bad, bad practice indeed, especially when they happen to admit candidly during an interview “Oh, no, I didn’t really know anything about that work, I was in the group so I got my name on it” – then why on earth did you insert it in your CV as relevant qualification, you dumb4$$?

I was shocked when a colleague recently said that after two years of work she had eight publications, plus countless posters and participations to meetings. needless to say, seven of those eight were of the aforementioned kind. And who on earth would care about which meetings and school you attended, unless you presented one at the first or were prized as best-in-class at the latters?

I try to put only first-author papers on my CV. which also implies it is desperately short. But at least I know I can defend that work with my claws, whereas if somebody is mifdly interested in me can always look up the other papers on pubmed or elsewhere and discover which fields I also happened to brush on. I probably know more than the average person in those, but don’t claim nor brag to being an expert about them.

Why am I doing this post, you may ask? Oh, because Nature just came out with a similar theme this weekend. With a wider view than mine, in fact, covering the responsibilities of co-authors on the scientific accuracy of the papers, real-world cases and so on. Go and read it, it’s certainly better than my rants anyway.

P – h – D

It’s done. Now I am legally a Doctor of Philosophy (edit: no, I am not – still a PreDoc). Not much to say about the viva, I did not really prepare for it and there was no need, at the end. It was just an informal chat on my work, mostly detailing small corrections to apport to the thesis.

Next step is? Who knows? Relax in Sardinia, celebrate, then… may be start to look for an alternative position. I have some idea in mind, I’ll share them in here very soon, as I get some more details fleshed out.

-2 to the Ph-Day

Only two days left before I face the panel, defend my thesis and hopefully get back home (via Brussel->Frankfurt) with three more letters in my business card.

To say the truth, i just want to get this over, I am not particularly tense for this, I just hope that the discussion will be interesting and science based, and I’ll get back home with not too many corrections, so to improve the final version before sending it to the printer.

Today, though, is a day busy with other things. Have to get to brussel’s midi market to get traditional sardinian sausages and cheese for my hosts in soton, then off to the station to grab my Euro* ticket. May be I’ll pay visit to some friends having a picnic in Tervuren, if I don’t feel to guitly. Otherwise, i’#ll read the final chapter of my thesis once more to preempt questions.

Failure to prepare is prepare to fail, said Gerry Halliwell.

Chiuso x Ferie

Truth be told, I’m on holiday from the blog ’cause I don’t have much time to devote to it.

Too much stuff to do at work, and with only five days left before the Viva I really am starting to get skittish about it.

So, it’s goodbye for the moment, and see you soon, after the exams and the well earned holidays.

I’ll try to split the blog in two or three branches, one where I’ll post about (my) science, the others i don’t know yet.

If I blog, I want it to be not just a diary but somehow useful to people out there.

First!!!

Lots of things have happened during this week.

I went to Lille, France, giving my first ever scientific presentation in front of a hiuge audience of three hundred plus medicinal chemists, slightly puzzled at my presence there.

I feel it may have gone better, not many questions were asked so may be I didn’t get my message through. Hopefully, next time will do better. The important thing is that the ice is broken, and I’ve shown to myself that I can stand up there.

Plus, most of the people met while there were quite interesting.

Second great thing, I finally have a date for my PhD Viva: the 6 or 7 of August I will be once again crossing the channel to reach Southampton, and defend my thesis in front of an internal examiner (not yet chosen) plus an industrial external (can’t disclose his name yet).

In the meanwhile, I am supposed to set straight my work record, by properly finishing the pKa prediction evaluation, and write up my Guinea-Pig CardioVascular paper.

lots of things to handle in so few weeks. we’ll see how I fare.

see you soon. Gotta go and mow the lawn, right now.

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 am LinkedIn

Linked in the great social network of Web2.0: here’s my profile.

It’s been a surprise t discover how many of my gmail contacts were already in it.

I thought I’d be one of the first one, instead two of my PhD supervisors seems to be aready there.

I wonder if it will be of any use for my future career.

Working on my Thesis

big mess. corrected one table before realising what it did talk about. this can only mean that the section which contains the table isn’t clear about it.

back to square one.

4th PostDoc Carnival.

The 4th PostDoc Carnival is up, at Minor Revisions this time.

This post pof mine (the most depressing of all) was selected…

Since when I posted that, situation has changed a bit, thankfully. With the thesis almost done, I have a better outlook to my future, although there still is a lot to do.

Papers from my PhD will have to be jotted down, following the outlines of the last two chapters – I do not consider the rest publishable – if not as a review – and that’s already out there.

Then time will be up for my “in silico prediction of CV safety” paper, something very much on the map of pharma journals since quite some time – and the Vioxx affair only put it in the spotlight once again. I hope to provide a useful contribution there. plus, it’s been fun, and it’s helped me to get known within the company – I am going to lecture the sister company in the following days, and hopefully I’ll fish a permanent position (I’m just moving in the same city, so that would help logistically too)

Finally, I’ve received a kind of direct invitation to go and present my latest work, a benchmark of pKa prediction softwares on our internal experimental database. The time frame for this is quite short though, I am not sure I will be able to make up a decent, nasty-question-proof presentation – no much stuff like this has ever been published and I understand why… every company has its own chemistry, and then, it isn’t an easy job at all.

Every time I think about it, I would like to change something in the set-up. just revision hell, I would never be confident to put my name under a title such as “To pKa, or to not pKa? An extensive review and benchmark of current commercially available prediction software.“

Ok, may be it would not sound that silly…

bah… we’ll see what comes up next.