The Power of Models

I'm going to break non-discolusre agreement, here... may be... or may be not. but haven't talked about my work for a while. I'm currently developing predictive models for generic cardio toxicity
to be used by chemist to decide which way to go when they are pondering about new syntheses. usually, they make the molecule, then send it to the biologists to test it against some protein target. ion channels in the case of cardio toxicity, the same proteins which lets ion in and out of the cardiac cells when your heart beats - if you stop them, goodye heart - and life too.
in vitro inhibition of the channels is good indication that something nasty may happen in vivo. so if the molecules come back with a red flag, well, they've had it, and it's back to the drawing table (and the synthesys bench).

but now there's another way. with my models, they do not have to synthesize the molecule any more - they can use the models I created (based on previous experience - i.e. on the data accumulated in years of trial and errors procedures) to see whether the molecule is active or not just from its expected chemical structure.

and the incredible thing is, it works! as good as the best ion channel inhibition test they've used until now.

here's a picture:

the three bars on the left represent the percentage of success of the three commonly used ion channel assays. Sodium, Calcium and Potassium. this percentage tells you that for example the socdium channel assay is consistent with cardiotoxicity for 80% of the time. whether there's or there is no toxycity, that is.
on the right, instead, the success percentage of two models I built, one based on bayesian statistics and arcane entities called fingrprints - the other one on chemical properties and the exotheric practice of Projection to Latent Structures by means of Partial Least Squares - Discriminant Analysis (PLS-DA for friends).
as you can see, both are slightly below the sodium accuracy, but the good thing is, you need to make the molecule for the assay - with my test, it's all done in one second or less within a computer... and this rocks!!!

see you soon! I'm going to enjoy a well deserved week end, now!!!

neck pain?

and before you think I'm complaining some more about my physical state, have a look at this: http://scienceblogs.com/pharyngula/2006/07/development_medicine_and_evolu.php

once again, PZ Myers at Pharyngula shed some lights on a very interesting piece of evolutionary biology...

had I had a biology professor as good as him, and not that pretty face of my teacher, I'd probably be in Richard Dawkins lab, right now... she had nice legs though... :-)

have a nice week end!!!

EDIT: and there's an update to the question, also showing how disagreeing and competing teams of scientists can nonetheless exchange data and information in order to solve the issue. at least until new data comes around to mess up the scene... GOD!!! I love science...

Live Wires

here's a scientist at Pacific Northwestern Laboratories that has discovered something very curious. some bacteria are able to conduct and exchange electricity between themselves.

don't really have time right now to comment on this. go and read the link... and have a nice week end!

what kind of animal is this?

yesterday I was going to prepare myself a pasta... never mind the recipe, what happened awakened my naturalist side and sidetracked me...

when I took the pan from the cupboard this tiny beast was in there...

Now, I have absolutely no idea of what it could be... it did look like a tail-less scorpion, but the big legs are in fact at the back... and from the enlarged piccies you can see that there's antennae at the front... I don't know whether the flurry stuff he's got all over it's natural, or it's put there on purpose... my guess is that it fell down from the wooden flooring of my kitchen cupboards onto the pan...
here's a few enlarged shots...



I spent a few minutes playing wit him and taking pictures, then it dropped on the floor and escaped under my washing machine...

if anybody could tell me what it is, I would be grateful...

tooth ache...

I'm plagues by pain since a few days... steady, and ennoying... can endure it but takes the joy out of life, really...
actually, it's more like a 'mouth ache'... my gums swell and the teeth close-by seems on the verge of falling (and a old friend knows how much I fear this)... my private doctor says it may be aftosis, but she hasn't really watched inside my mouth... mah...

anyway, I'd be tempted to shot a piccie with my mobile phone, and post it... but I'll spare you... god it hurts... see you soon, I'm going to buy a mouthwash...

unexplained diarrhea

No, it's not me to be sick. nor is anyone I know... just wanted to point your attention to this interesting post aout an unexplained epidemic outbreak of Diarrhea. from aetiology, as usual... the post, not the diarrhea... you silly... :-[

Campioni del Mondo!!!

do I need to say anything else? I'm sorry for the frenchies who read this blog... or may be not. we won fair and square.

outsourcing FROM india...

you read well. not TO india, but FROM india... apparently, faced with a shortage of skilled labourers in the arts conservation business, india will outsource part of the workload to private agencies elsewhere... funny uh? we export high tech (and call centre) jobs there, and they export back... original post from The history Blog. What? did you think that I only read about science and stuff?

The Elegant Universe

I thought I'd share this. a three hours long documentary about the Theory Of Everything (TOE), Strings and hidden dimensions. Haven't watched it yet, but looks good.

thinking about... boobs...

or, more exactly, mammories... I bought a new T-shirt on saturday: the drawing on it is... well, here's a picture of it:
the picture of the little mammal sucking his mother's tits got me thinking... how's it that cows have their mammories close to the hind legs, while women have them closer to the upper part? I can see a clear advantage for the primates to have nipples on the upper body - it make it easier to keep their infants with the hands - young veils/zebras/antelopes do instead walk on their own...

but... how the position of the nipples is decided during development? I always thought they were 'linked' to the chest, but that's very anthropomorphic... I wish I had an evolutionary biologist at hand to ask him... may be I should contact Richard Dawkins... or may be PZ Myers will answer...

Kayaking is fun!!!

just back from the ardennes, where I did my first twenty km of kayaking... it's incredibly nice but I would go somewhere else if I were you... too many people in Dinant, there were something like 1k kayaks on the river, it did look like a city centre traffic jam... no capsizing, nor other unpleasant events, for me at least. pictures to come later on... have a nice week. and Go!, Italy!!!

Blog of the week

here I am again... to suggest you another blog to check out: Aetiology, by Tara Smith. it's part of SEED's scienceblogs constellation, and extremely interesting: it talks about bacteria, diseases, and such... from both a medical, and biological / evolutionary perspective... well, see you soon... you know I'm going to post again, right?

again on movies...

the previous movie-related post started something in my mind... which book/comic would you like to see (decently) translated in celluloid by next year? if I were to pick one right now, I'd probably say The Reality Disfunction. there's enough material to shoot three movies, there's plenty of charismatic charachters (Al Capone, for God's sake), plenty of Hollywood-style action, spaceships, whole fleets of them, anti-matter weaponry, culture clashes (between Adamists and Edenists), and then more: Nanotech, Aliens, there's even Zombies!!! it's a free-for-all extravaganza. and it also works out pretty well. There's a princess in a high castle, although the blue prince is a bit on the cheap side, and at the end he goes with another girl - good old fashioned english upper class girl... did hamilton manage to leave anything out? it's "The importance of being Earnest" meets "Gone with the Wind" meets "Battlestar Galactica"... Uhm, I better go to work now... but if you want to jot down your favorite conversion, please do so. and good afternoon ;-)

a night to the movies

yesterday I went to see a movie... any movie, "she" said... of course in belgium movies are either in french (dutch subtitles) or english (dutch and french subtitles - essentially, half of the screen is wasted)... that does not make me particularly enthusiastic about going to movies, I have to say, coupled with the exceptionally belgian attitude that, after paying the ticket to enter the cinema. they expect you to pay if you go to pee, too. crazy people... I just hate that.

anyway, due to my languages restrictions, only movies in english were in the rose of candidates... and I already saw CARS (good!), and Ice Age 2 (not so fresh anymore)... not that my sweet half would compromise on going to see cartoons, of course they're for children... yeah right. have a look at Barefoot Gen... Oh God I lost my thread... Oh yeah I remember, ok long story short, I went for 'The Da Vinci Code'. I know it was stupid of me, but could not resist... I mean, ok Yom Hanks is in it, and that's a big minus, but Sir Ian "Magneto" McKelln, and most important of all Audrey Tatou!!! Oh yeah and that frenchman, what's his name? Leon... Uhm no... not really...

Anyway, went in very much convinced that i was going to be bored to death... and I was not!!! I thought I was going to laugh at the risible plot, after a dear friend told me that in Agels and demons CERN is depicted like a double-face organisation kind of the X-Men academy, sporting a mach 15 jet... well I was expecting to see crazy things like the pope slaugghtering people with a light saber jumping up and down inside san pietro. kind of Yoda in SW ep III. well may be not that crazy... None of all this instead. a very measured and well paced plot, even if too long... Martin Mystere would have managed to fit it within 140 pages, I'm sure... it actually did...

never mind however, it's a movie that you can relax in the armchair and enjoy. but I have not read the book, so please don't come and say "It was soo different"... Hunt for red october was incredibly different from the book, but it still is a good movie. as it is V4Vendetta, despite its dissimilarity form the comic book...

Ok, have a nice day you all (two o three person I presume) who are reading this blog...

Gufo a.k.a. Luca a.k.a. The Menace (by janssenn's girls apparently- someone has been spreading rumors, damn him)

Did I took the wrong path?

Sometimes I wonder if I shouldn't have gone to biology, rather than chemistry, during my studies. It certainly seems so from my interests... just have a look at the previous posts in this blog... and the books I read, and those of you who knows me in person
know how much time spend wondering about dinosaurs and such stuff... a lot...

well, I wanted to do biology or physics but the first one wasn't very promising at my place, and the second one was out of discussion - no physics degree at my place, and not enough money to go anywhere else. So I did chemistry, good compromise in between the two and with good employment perspectives... and after the Comp Chem specialisation I've been slowly transitioning to biological sciences... with a computational twist all the way around...

who knows what the future holds for me?

The Black Death is back...

Here's an interesting piece from Tara Smith at Aetiology. A Plague outbreak in Republic of Congo... She already told us about a woman in california who got plague some time ago... Check out her blog 'cause it's incredibly interesting... (and she's pretty and has tattoos too) :-)

And if you want to help out with the outbreak, I guess you can do your part sending money to Medecins sans Frontieres...

did you ever wonder...

where your gills have gone, when your grand-grand-parents became ground-walking animals and didn't need them anymore? Until now, in my ignorant chemistry-oriented world vision, I assumed they became our lungs... but no, actually. they became our neck glands, and face muscles, and part of the jaw... I mean, how cool is that?

Can you clone schrodinger's cat?

Interesting idea, but I'd rather have started a Lorentz's butterfly farm to become all-powerful king of storms...

Remember, remember, the fifth of November...

I've seen this movie in the weekend... WOW! It does rehabilitate the wachowsky brothers in my view of the world. After the awful mess they made with the matrix... I don't remember the comic book well enough to say whether the plot of the movie was 'TOO" different, but it ceratinly did give me the same emotions. all the important parts have been kept, the action (esp the Kung-fu sequences) is not excessive, the acting is good, the sfx and scenery wonderful and the whole movie only drags a little in the third quarter... but I wholly recommend it!!!

my brain is wired the wrong way around...

hey, some people at UCL have discovered that we use the same part of the brain to speak different languages... it just switches back and forth from different modes... I could've told them so
from long ago, since now that I know english, every time I try to speak french
some english words trickle down with it... I guess my brain's switching system doesn't work properly... my parents would probably say that this isn't a surprise, either...