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.

MOE's LigPlot gizMOE rules!!!

I just tried to use MOE (Molecular Operating Environment) to draw a ligand/protein interaction diagram. I fell in love with these kind of graphs the first time I saw them, from the original LigPlot software. I love the way they represent the fundamental interactions without the fuss of 3D structures. I did once suggested the use of them rather than confusing 3D structs as output of a distributed docking program at my previous university. Look at the picture above, and it shows how a given ligand interacts with neighboring residues by means of hydrophobic contacts (the small sun-like drawings) or hydrogen bonds (the green line with distances)

Anyway, right now I just needed a couple of shots showing how the lipocalins' binding pockets are devoid of h-bond anchor points, if compared to other classes. Unfortunately, LigPlot for windows does not come without the hassle of having to mail his author, so I had to wait until I got back to work. Where we have MOE and their own implementation of the cake.

This morning, then, I loaded up three Lipocalins structures, plus one Exopeptidase, one Protease, and one Oxido-Reductase for comparison and hey!, presto, I have six wonderful shots lending weight to my assertion.


(picture here isnone of them, just a snapshot from MOE's website - again, green lines show h-bonds (without distance, but they have directionality as added bonus) - the green balls are apolar residues in hydrophobic contact.) I am not sure what the blue line is. Oh, there it is: When the hydrogen bond is formed with the residue sidechain, the arrow is drawn in green. Hydrogen bonds to the residue backbone are drawn in blue, with an additional dot drawn at the residue attachment point.
I just wish my current work was more structure-based to be able to play some more with all these cool softwares. Well, may be my next job? or life? who knows?

Plan for the week.

Finish off thesis.

Work on CV paper.

Look at In Vivo Clearance data.

Blog roll if I get a chance.

read up on xkcd the new (for me) webcomic I just discovered:



Solve this damn riddle...

Oh, I also have to catch up on Freefall and PennyArcade, if I get a(nother) chance.

Like Old Yoda my computer wants me to write

sneak peek at my PhD thesis (almost ready - now you know why I haven't posted the last four days) where Word's ortographic corrector suggest me some rather strange re-arrangement... I thought about writing all the post with inverse syntax but have not time right now... got to finish it. yet, I can't let it go... One last check... one last-minute addition... will I ever get rid of it? Stay tuned!

Nothing much to write about.

Slow start of the week, this one...

Am trying to wrap my head around the CV paper, but in fact my thesis is at the prime place. tonight I am due for a couple of hours (at least) of tireless corrections. The idea is to get it done by the end of this week, helped by the fact that thursday and friday are off-work.

Then, there's the move to the new apartment with the lady, which will take up most of my energies.

On the first of June we should be done with cleaning up our old apartments, and possibly putting up the furniture in the new one. The 2nd I am off to Amsterdam for a gawdy trip with my work colleagues, and the day after I'll try to cycle some 40km with my gf's workmate, and nientepopodimeno che Eddy Merckx!

Oh, don't think it's done yet, 'cause the 5th of June I'll be showing off what I've done to a Janssen consociate in Mechelen, Tibotec, where I do hope of landing a permanent position, sooner or later.

Ah ah haven't finished yet: first draft of the paper is due for the 22nd of May, the day after I leave for a week-long course in Oxford, where I'll also meet up some sardinian colleague who've settled up there.

Sounds like a plan. I wonder if I'll manage to squeeze in some holidays for July.
:-P

Can't Bloody Sleep.

No way of sleeping, after three o'clock tonight. must be the emotion of finally getting back my whole thesis corrected. Now I only have to incorporate the final changes, one or two tables/ graph and off I go, toward a luminous future.

First though, I have to use the company's facilities to shave and shower myself. see you later!

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.

Back To Work!!!

It has been a nice weekend. And, surprise, people have kept coming along to read this blog, apparently, even if I didn't post anything at all in the last four days. Too busy having fun, eh eh... It seems like there's a critical mass for blogging, once a certain number of bloggers link to you people will keep coming. I wonder if anybody has done any serious study on this?

Anyway, I was planning to go to Liege on friday, but I did not. too much hassle and my GF wasn't free. So, I held off and went looking for my lost mobile. Which I did not find. pants! just what I needed, another 200 euros down the drain... Pah!

However, the rest of the weekend worked out as well as planned, or even better. Enjoyed a half day shopping on saturday, then on sunday, while Marie was on call at the hospital, I went away with some friends, cycling 40-odd km from BXL to Tervuren, running round there and then back. Pictures below:

Tervuren-29Apr07

As you will be able to see, I did enjoy having some duck families close-by. Yes, I said duck, not dutch. Duck! As in Donald Duck. Although the exact species was unknown to me, and most likely different from our cartoon hero.



Here shown in his typical emotion, rage.

And moving on, the following day was BBQ day in Liege, finally, with some italian friends and their arab boyfriends. It looks like all italians abroad are going for mixed couples. Good. We definitely more italian attitude in the world.
The following morning, once the fumes of portuguese and french wine (and the sardinian traditional fruit-spirit, Mirto Rosso) cleared away, Marie and me jumped on our bike for a short up-and-down hilly road, whose surrounding grassy slopes were dotted with herds of cows. Again, pictures follow, no comments on these ones:

1stMay07

After that, a quick lunch and back to Bruxelles, with stopover in the characteristic university city of Leuven, aka Louvain in this crazy, two-and-a-half-lingual country.

Here you can see his gothic-delyrium city-council palace (Hotel de Ville).

That was it. Now, I am back to work, with tons of mails to wade through, my soon-to-happen move to Mechelen to organise, a series of dutch lessons to plan, a post-doc lunch to take part and a Physiologically-based PharmacoKinetics seminar to follow immediately after. not a lot uh? I better check Gastroplus manual.At least I'll know what Stefan is talking about...

Oh, and I also have to set straight my pKa assessment, and find out exactly where half of my acidic pKas went down the drain of forgotten compounds instead of being carried on properly. And will have to subdivide the sets in mono-acidic, mono-basic and so on. Sounds like a plan.

God helps me. Or, the FSM helps me. I haven't done much progress in readuing his bible, my attention was stolen by the latest book I bought "The Wisdom of the Crowds", a fascinating and assertive book on the virtues of letting people (as in plural) make up their mind, aiming to show how this kind of unsupervised free market of ideas, and any other thing usually comes up with the right solution over time, whereas the experts in ay given field do get it wrong more often than not. I blogged about it in my previous post. Interesting, I've always been opposed to popular referendum and this kind of direct democracy, based on the assumption that people mostly don't know what they're doing themselves, let alone are able to decide on complicated matters such as "is nuclear power an economically sound way of generating electricity for our industrial base?". But if, as it seems,. the author backs up his assertions with solid data and numbers, not only with andoctal evidence, we may be onto something. Also, it comes to my mind a paper in the field of my PhD, Docking and scoring function, where it is shown that consensus scoring (that is, merging the suggestions given by different programs on deciding whether a molecule is going to stick or not to a protein) works better when it is applied 'by-number', and not 'by-vote'. It would make sense, in the view of this crowd wisedom thingy. If I get the time, I'll try to explain it later. Now, let's work. See you soon.