Why would you want your doctor to have studied evolution?

the 4 best answers are here.

and, from here, congrats to Gregory Simonian for winning!!!

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!

I've got to get back to the Gym...

This summary is not available. Please click here to view the post.

Herpes learns how to play nicely...

Or, integration steps of a former parasite:

The conventional view of herpes virus infections is that they are either active and harmful, or at best silent and for the time being harmless. But new work on mice suggests a third option: there may be a direct benefit for chronic herpesvirus infection. Latent infection with the murine HV68 confers prolonged cross-protection against a variety of bacterial pathogens, including Listeria and the plague bacillus. The protection is a result of systemic macrophage activation triggered by -interferon. The latent virus thereby sets the level of innate immunity. Not only is latency an active immunologic state, but this activity provides symbiotic benefit.

Taken from Nature's latest issue.

Something that Carl Zimmer will likely write about.

Subscription day.

Inspired by PZ, I subscribed to MySpace and Facebook, although I doubt I'll ever use any of them. Most importantly, I subscribed to the Nature Publishing Group website, just to be part of their Nature Network.

So, if you check the tag for ADME, I'll be there.

And I'll be there for Docking and Scoring too.

Let's see how it turns out. Certainly, this one will be my main blog. Don't have time for another one, for sure.

Still, it is a very nice idea 'cause at the meetups it is possible to meet scientist and like-minded from all fields, and not just your own playground or university. I foresee lots of discussions, and hopefully there will be a Brussel section to which attach for me.

Whoah! Is the whole net like this?

If I look at my blog's visits, more than half come from Firefox!!! This doesn't fit with my idea of Firefox still being minoritary. Is it that my readers are more technically minded than the average internet user? Well, kudos to you for making a good choice, then.

I Just want to visit this place:

courtesy of Botany Photo of The Day

Yeay, that's what I am talking about...

Coturnix has a nice post about a favourite childhood book series of his, but most specifically on the pyramidal scheme of information dissemination used by the three detective boys in the books to gather information. Every boy would phone up to five friends, and they would answer the question or in turn phone five more, and so on.

This comes just right with my discovery of Yahoo Answers, which sucks when you want some scientific knowledge but rocks when, like this morning, you want to know what kind of shirt color I can match to a brown suite and black shoes and belts.

For Science, seed is much better, as are many other places.

Pyramid schemes are a very efficient method of disseminating information, although they came at the price of disseminating it to a majority of people who most certainly do not know the answer asked for.

In the book that I am reading, "The wisdom of the crowds", the same thing is pointed out for decision making: although aggregating individual decision in a collective one is a very good way of finding the right solution to a problem, in practical terms this isn't always possible. It's often better if the decision is left to a group of 'expert' at the condition that they be diverse enough, and they do not influence each other by being aware of the decisions made by others at different times (a phenomenon known as 'cascade').

That's the limit of what's called partecipative democracy, i.e. a political system where every decision is taken through a vote by the citizens. The parliamentary alternative is not necessarily better, and if the theory underlying the book is correct, it would be better for us to randomly select our representatives than to elect them. this way, we'd get a better cut of the population. Now, I am not one hundrd per cent sure but I believe this is how it happened in at least one country of the past, where the member of the "senate" were drawn and had the civic duty of leaving their jobs (I believe with compensation for it). Much like the juries system in the US. May be it was Athens? I don't remember.

Anyway, all this seems to be ticking together, I really love when I find myself involved in such synchronicities.

Yahoo Answers Again and Again...

I am having a blast

I recently registered to yahoo! Answers website. I just needed to find out whether or not my mobile phone would support a given bluetooth protocol.

The website is quite useless for that kind of thing, and seems overrun by teenager looking for answers (duh!) to either existential, or very stupid questions. some even try to make their homework this way, a very dangerous practice. I would never trust an answer given on such a website. Here's why. I have a wicked sense of humour, so it didn't take me long to end up, jumping from one question topic to another, in the "religion" subsection.

And there started the fun, when I saw silly flamebait questions such as:

Muslims- do you support your anscestors killing hindus and breaking their temples down?

If your a mother/father what are your kids reactions to them finding out that your either gay/bi/trans, etc?

Bible want to shave women if they do not cover head. Does bible interested in undershave also?

Is death the end of conversation ?

O Christians, how you pay the royality of each edition of bible if it is word of god?

Glorious Quran is universally one and purest word of God. Why each bible differs with other one?

Isn't this great? I started writing puny answer to each and every one, until... I hit the daily limit!!! LOL!

Now I can stop and go on to more serious business, such as actually doing some paid work, or finish writing up my thesis. time to grow up. ghep.

new piccie of the month widget on the side bar...

Thanks to John Orcutt at Oregon's Trail for the idea.

I will start with one of the most beautiful spots in my island: The Stintino beach, on the extreme northwest of Sardinia, once fishermen village and now holidays' hotspot.

google maps link. (hopefully, one day I will manage to directly link google's map piccies.

BlogRoll

Check out Tet Zoo for yet another of Darren's nice pieces on lizards.

He also muses on some huge pig of Georgia, too.

Pharyngula has been absent for quite a while from these pages, but now's back with a vengeance: from there, a cool movie about insect being slo-mo thrown pies and juices at while flying/walking. Plus, the tragedy of an astronomer incompetent enough to believe in ID.

Secret Sex Lives of Animals is now in my permanent blog roll, go and check Kate's piece on bedbug piercing each other during sex, strangely reminiscent of Dr Tatiana's piece on the same subject. She also has more soft porn on Panda (from the BBC).

But the grand stand is for Carl Zimmer, who has two wonderful posts (no, full articles) on Papilloma Viruses evolution and on the completion of the 'Possum genome and what can we learn from it about our own place in natural history.

Wonderful wonderful job everyone. Kudos!!! I really enjoy your writings!

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

28 (insert period of time) later

I loved 28 days later, by Danny Boyle. I was living in England at the time, so it made much more of an impression. Although, not quite as much as his funny sibling Shawn of the Dead. The idea of few survivors in a wasteland seems to work particularly well in England, I don't know why.

Oldest thing I can remember with this subject is The death of grass by John Christopher. Then, of course, 1984 by George Orwell, V 4 Vendetta by Alan Moore. There's more probably, but can't think of any right now. Something from Greg Ballard may be - although he's never been in my favorites' list. Oh yes, let's not forget the greyish Children of Men. Oh yes, The Day of the Triffids

Anyway I was disheartened when I discovered that the Americans were shooting 28 weeks later. It did seem like a foolish follow-up - Quite frankly, I though it was going to be crap.

But then, I read the NY Times review of the movie, surprisingly positive, and I understood (once more) that I seem to be unable to catch analogies - and here the focus of the movie is to show the relationship between the american occupation troops and the surviving UK population, being reintroduced in the de-populated cities. and what will happen if those undefended people turn out to be re-infected, once again, in a situation parallel to the one in Iraq where everybody could be a suicide bomber.

Clever uh?

May be I'll give the movie a shot. If it's only half as scary as the previous one, It'll be well worth it.

A final word: God I wish that someone made a movie out of the death of grass.

spiderman 3 really doesn't take off.

It's still stuck at 6.8 on the imdb. Well, at least it's not down to 5.3 as Ghost Rider is.. Still, it is definitely below what attained by the first two installments. Actualy, the second one went better than the first one - I would agree, with the exception that the bad guy did suck - but all spidey's bad guys suck, I think - Unless he fights someone else's enemies, like Victor Von Doom. Well, I am getting curious now, may be this weekend I will shell out those 12 euro to go ad watch it. After all, movies like this should be seen on a big screen.

BANG!!!

Some stars really go with a bang, suggest this new research reported by the NY Times:

The cataclysm — a monster more than a hundred times as energetic as the typical supernova in which the more massive stars end their lives — might be an example of a completely new type of explosion, astronomers said. Such a blast — proposed but never seen — would explain how the earliest and most massive stars in the universe ended their lives and strewed new elements across space to fertilize future stars and planets.

“It is quite possibly the most massive star that has ever been seen to explode,” said Nathan Smith of the University of California, Berkeley, who estimated the star as “freakishly massive,” about 150 times the mass of the Sun.

And here comes the scary part:
The star bears an eerie resemblance to one in our own galaxy, Eta Carinae, which has been burbling and bubbling in the last few centuries as if getting ready for its own outburst. The observations suggest that the troubled and enigmatic star, thought to weigh in about 120 solar masses, could blow up sooner than theorists had thought. Mario Livio a theorist at the Space Telescope Science Institute who was not involved in the research, said the death of that star could be “the most spectacular star show in history.”

Well, let's hope it doesn't happen before we've got ourselves out of the cradle-Earth. Such an explosion may sterilize completely the planet. Ouch! Well, there's no reason to worry about something we can't avoid. Yet. One day, I foresee people prodding almost exploding stars like children prod sleeping dogs with sticks. Hopefully, the star will not chase us to destruction.

if (prenatal_diagnose == down) then abort()

as described on the NY Times, almost 90% of unborn children diagnosed as having down syndrome are subsequently aborted by the parents. This seemingly puts at risk the remaining down, as their dwindling numbers will mean decreased visibility, therefore less money spent on support programs and such. May be, though, we'll have more money for those few children who are born with the condition? which one is the right choice, in your view?

I am internally fighting over this. Quite frankly, I don't think I have the balls to raise such a child. We discussed this over a couple of times with my GF and I'd rather abort. She would rather not - on the other side, she said she would not force me to be parent this way. So, my personale choice is quite clear. I'd rather have a healthy children, than a down one. However, I see the point in the agenda of the already born down's parents. Less down children will mean less visibility, therefore less money going toward research programs. Support program will continue to exist, yes, but research is a different thing. A drug needs a minimum investment to be made, and if the market is lower, the rice will be higher. same can be said for new techniques and such. therefore, a decrease of 90% in the newborn downs strongly puts to risk the improvement of thos who already are there, who will get no more new treatment as their numbers do not justify the expense any longer. I am surprised by the high percentage too. 350000 in the whole of US means almost one every thousand people is down. That's a lot more down I use to see. May be in Italy they are kept away from the view?

Anyway, lots of food for my mind. and yours.

Featured in the (bad) press

Uh Oh, The NY Times has a very nasty piece on the American branch of J&J and AM GEN who've apparently been paying (a lot) doctors to prescribe their anti-anemia treatments (EPO, a.k for its role in cycling doping).

Here's how the trick works.

Doctors buy from the company 9M US$ worth of drug. They prescribe it to the patients. Insurance or Medicare pays (let's say) 10M US$, to cover the drug's and all other costs. The company who sold the drug, though, send the doctors a rebates worth 2.7 M US$. Profit!!!

Frankly, I am disgusted of these practices, especially knowing that the company I work for (one of the two) prizes itself so much over his own credo. Now, I know this kind of practices are legal in the US, still this does not make them morally acceptable. Bleagh.

Do Penguins topple when Planes fly over?

I found this while looking for a penguin gif:

On November 2nd timothy of Slashdot asked if penguins topple when planes fly over? The British Antarctic Survey has organized a the first expedition to explore this theory and came back with news now.

The short answer: No, penguins don't fall over.

In November the BBC released a story covering a research project that took UK scientists to the South Atlantic. They wanted to discover if there is any truth in the tale that many aircraft pilots told the public.

Pilots often reported that when they were flying over a colony of penguins the birds were watching the planes, but instead of moving their bodies to follow the aircrafts they only moved their heads which lead them fall backwards over. This was said to happen to the entire colony of penguins and not just to some individuals.

If this was true, it could lead to a serious problem. Penguins only live in colonies around the antarctic and there aren't that many. If the aircrafts disturb their breeding pattern future of penguins is uncertain. The research project was acknowledged by fears that breeding patterns of the birds may be disturbed and interupted by aircraft activity such as jets and helicopters from aircraft carriers.

From the beginning of this research project there was no evidence that penguins actually fall over. All the scientists knew about were myths of aircraft pilots who supposedly watched entire colonies topple.

The researchers from the British Antarctic Survey went to South Georgia, an island belonging to the Falklands, in order to observe a colony of King Penguins. With help of the Navy and their ice patrol vessel HMS Endurance the scientists let helicopters fly over the colony of penguins and watched the birds.

The results were different from what pilots formerly reported. The birds did not fall backwards over or watched the helicopters. Instead the penguins went quiet and some moved away from the disturbing noise. Though, after the helicopters were gone the penguins moved back to their regular places. Please read the entire report.

Frankly, I can't believe they really went to check!!! LOL

more info here.

Paper time

I have finally started to write up last year' pice of research into a paper. The intro is done, mostly, and a quick draft of the data retrieval and preparation is in progress. Of course the lion's share, results and discussion, are still in my mind, in a yet unshapely form.

Want to know what I am going to talk about? In general, Cardio Vascular safety issues in Early Drug Discovery. More specifically, my in silico modelling of the Guinea Pig Right Atrium Assay.


Hopefully, when I'll submit it to J. Med. Chem., where I believe it belongs, and which has a nice Impact Factor, it will get accepted for publication. Finger crossed.

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!

Filling up my sci-fi bag

I am buying these books. That is, I will if the server at play.com stops hitching up.

The Time Ships - Stephen Baxter

Exultant - Stephen Baxter

The Swarm - Frank Schatzing

Enjoy your evening!

Alfa 156 SportWagon

Here's my car, in all its splendor in its own wikipedia page. It's the 1.9 Diesel 85 KW (115BHP) 2002 facelift model.

nice website for mobile phone users

http://www.mobile9.com/ <-> I just downloaded a series of ringtones, screensavers, and Java apps and games. I thought I'd share.

Z!

I am sleepy. I think I'll lie down.

I've just seen Desperate Housewives season 3, ep 21 - too sentimental for my tastes, with Susan getting lost in the woods and Linette falling (almost) for the handsome cook. The worst part is, the ending of the episode was even worst. Yuk!

Rotten Tomatoes

I found their top 100 movie list. It looks like the people there have a special eye for the past, as I don't know most of them, if not just by name...

They also have a top sport movie list, although this is far too heavily american-centred, with so many movies about baseball and the US version of rugby, called football even if they almost never use the feet to drive the ball (?). And, quite frankly, I'd have taken down talladega nights (which I loved) to insert a few other, like "There's Only One Jimmy Grimble" or even better "Cup Fever".

And, as you can expect, I don't really agree on their "Comix Worst to Best" List either.

Let's see if they have any sci-fi flick list, too...

More Spiderman 3 reviews

Uh, it seems like my post on spiderman 3 and the kinda lukewarm review it got from the NY Times generated quite a number of hits.

So, here I am to cater to the interest opf my readers. I've gone out looking for more info.

On the IMDB, spidey gets a decent 7.1. That's the people's vote, but keep in mind that this is people who bothers to vote for a movie after seeing it, so it's likely to be composed of a higher than usual percentage of fanboys, both pros and cons. Hopefully, they cancel out.

If you look at RottenTomatoes, instead, critics average on a somewhat lower score: 61%. Tomatoers do score it more or less like IMDBers, at 66%. Are they harsher? uhm,. judging by the average age of the top 100 movies in the two databases, I'd say they're older, less Matrix-generation and more Casablanca: may be less fanboyish, or just more classic oriented. I do tend to agree on them, meaning that a movie can only be called a classic when a audience born 25 years later than the movie itself still likes it.

Back to spiderman, I guess I'll have to see it, but for the moment only CAMs are available for download. may be in a couple of weeks some decent DVD rip will hit the pirate bay. Until then, I'll wait.

here's the trailer anyway. (update for a better trailer)

Bellezza in bicicletta

Quando, a primavera, per le strade
passa il "Giro" gridan tutti ai corridor:
Dai, dai, dai, dai, dai, dai!
Dai, dai, dai, dai, dai, dai!
Ma se una maschietta in bicicletta
passerà vedrai che ognuno, là per là
la testa girerà e allegro canterà



Ma dove vai bellezza in bicicletta,
così di fretta pedalando con ardor?
Le gambe snelle tornite e belle
m'hanno già messo la passione dentro al cuor!

Ma dove vai con i capelli al vento
col cuor contento e col sorriso incantator?
Se tu lo vuoi o prima o poi
arriveremo sul traguardo dell'amor!



Se incontriamo una salita
io ti sospingerò
e stringendoti alla vita,
d'amor ti parlerò.

Ma dove vai bellezza in bicicletta,
non aver fretta resta un poco sul mio cuor
lascia la bici dammi i tuoi baci
è tanto bello far l'amor!



Ma dove vai bellezza in bicicletta,
così di fretta pedalando con ardor?
Le gambe snelle tornite e belle
m'hanno già messo la passione dentro al cuor!

Ma dove vai con i capelli al vento
col cuor contento e col sorriso incantator?
Se tu lo vuoi o prima o poi
arriveremo sul traguardo dell'amor!



Se incontriamo una salita
io ti sospingerò
e stringendoti alla vita,
d'amor ti parlerò.

Ma dove vai bellezza in bicicletta,
non aver fretta resta un poco sul mio cuor
lascia la bici dammi i tuoi baci
è tanto bello far l'amor!

mp3 here

Kite!!!

Lazy day today...

having lost my mobile phone, I am off to the provider shop to get at least a sim card replacement. may be buy the same model of phone too (SAGEM), if nothing else better has come up. I doubt it. This way, I'll also have duplicate of all the accessories, which can't hurt when living in two distant places as I do. Even when I move with my GF, I'll keep one at work. or in the car, just in case.
the other option would be to grab a mor eknown brand, like NOKIA, so that i can grab third party accessories more easily.

Before,though, I want to explore around by bike using the GPS as tracking device... If I can get it to work that way.

And then once I get to BXL, I'll buy a traction kite (the one shaped like parachutes)
since I left my delta kite in the mountain's house of my GF's mother.


In the evening, I'll meet up with freidns and possibly my lady to go and see an italian representation at the theatre, "I promessi sposi" by A. Manzoni in the parodical version made by the Trio "marchesini-Lopez-Solenghi", a two-man+one-woman comic actors group from Italy.

That's it for me. Have a nice weekend.

Where's the number everybody is talking about?

Is it here? Nope. But I found it here yesterday. Today isn't there anymore.

may be here?



Dear AACS, You can't stop the signal!!!

09 F9 11 02 9D 74 E3 5B D8 41 56 C5 63 56 88 C0

Where do you come from?

here's a screenshot showing where the visitors of this blog come from. Curtesy of google Analytics. Apparently, american and british love me, italians and belgian tolerate me, the rest of the world is mostly indifferent. Well, it could be worst.

Apparently, spiderman 3 sucks

At least this is the conclusion of the people at the NY Times who just saw it.

Well, I will wait for aXXo to release it on the torrent.

Allo Allo

Hi, Just a quick post on a new (actually, vintage) TV series I discovered recently.



In the word of the BBC comedy guide,

'Allo 'Allo! was a direct-hit domestic sitcom and huge international success that made a star out of its lead, the funny and talented actor Gorden Kaye. At first sight, frolics in Nazi-occupied France may have seemed a dubious subject for humour, but the show's premise was not to make fun of the war but to spoof war-based film and TV dramas.

In my words, it's an incredibly funny and well built sitcom, with plenty of crazy characters. It manages to give the nazis a human face, I absolutely love it! All characters are involved in a network of (half-assed) intrigues, who binds them one another. Every single one of them is sucked into this maelstrom as soon as it enters the little cafe`/restaurant that Rene`, the main character, runs.

I am currently viewing the second half of the first series, and enjoying every single moment of it! 9/10!!!

here's the first part of the pilot episode, from youtube

Synchronicity

I read a post about Prototherian mammals, today. Prototherian, the only clade within Monotremes, are mammals ('cause they make milk) but do still lay eggs, like reptiles. The post is up here at fish feet. There it is!!! There's a nice piccie of a Playtipus, one of the two protherians still living today.



And hungry for new things to read/post, I went to see today's featured picture on Wikipedia, and surprise, it's the other prototherian!!!



Synchronicity, as Carl Jung would have called it: ...the experience of two or more events which occur in a meaningful manner, but which are causally inexplicable to the person or persons experiencing them. The events would also have to suggest some underlying pattern in order to satisfy the definition of synchronicity...

So, do plants fart, or not?

a paper came out some time ago revealing that plants do seemingly emit large quantities of CH4, a powerful greenhouse gas. Conservative people and newspaper in the whole world (weel, ok, just in the US) souped it up concluding not only that human weren't causing global warming and plants were, but even that to save the planet, we had to burn down as many plants as they could, and deforestation and such were morally justified. I don't know how this would justify driving a big ass SUV though, or squandering water and other limited resources. pah.

Anyway, a new paper refutes the first one, showing no significant emission from living plants. Carl Zimmer has more details about all this. With a vengeance. Go and check it out. I'm going home now, and will try to cycle without farting. You never know.

Creationists attack Chemistry!!!

thanks to Interrogatin' Nature, which I just discovered (thanks to Sarda, whose blogroll post inspired my previous)

Blog Rolling

I've been too busy in these days to keep up with the bio-blogging scene.

Only the usual suspects made it to my attention:

Darren Naishm, over at Tet Zoo, talks about tortoises' penises, but also present his (yet) unpublished field guide to British Ostrich Dinosaurs (first part here).

Carl Zimmer, as usual, plugs his own pieces on the NY Times, about duck penises. I spot a pattern here. Oh an important thing I had missed at first: he is pointing us to significative articles he wrote, one per year, stored in his own repository. (I still have to finish Parasite Rex, damn. Too many good book I am juggling right now)

Laelaps it's always nice to read, but haven't checked him out properly yet. this afternoon.

Last, but not least, Sarda at Fish Feet explores the real estate market of stone age britain. Apparently, the Lake district were a favorite at those times too. Oh, she also writes about the deatmatch to end them all: Shark vs Dinosaur!!!

Did I leave anyone out? Oh yes, the newly discovered Secret Sex Lives of Animals, a blog whose name says it all, written by a beautiful evolutionary biologist. I mean it. Actually, now that I've seen some pictures of Olivia Judson on the net, I wonder whether this isn't her blog? Judson, Hudson...

that's it for the day, I hope you'll enjoy!

You are here, in the lower left corner

thanks to the BBC for this (pdf) map of the last 180 Million years of animal evolution:

I didn't know we were so close to rabbits (lagomorpha)


below a piccie of the complete version. Hopefully, I'll manage to dump it as hi-res jpeg and post it (update: I can not. even if I could, the font size the species names are written with is tiny tiny tiny).

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.

It's hot up there...

It's been two, no three weeks without rain, a very unusual thing for spring, here in belgium. It's so dry, that I need to water my rucola, and it's so sunny that it's growing large, and bitter like hell. So, I have been sitting in my GF's garden, basking in the sun and eating a nice mediterranean salad.
Yet, something feel wrong, with this weather. A friend told me that the Azorres' anticyclon, tha high pressure area which usually hovers over the mediterranean, has moved up north, while the souht of europe is blessed by sub-tropical rains. I don't know if this is true, but it certainly is worrying, and I believe I am not the only one worried. not that I see many people tearing apart their clothes and stopping using their cars, yet. Well, tearing apart their clothes yes, but only to sun-bake themselves to death. The average belgian has now a color which makes them look a bit more of an arab, and a bit more of melanoma too, in the near future.


And there you are, the NY TImes as usual reports that the artic sea ice cap is melting faster than previously thought. Woah! Here's the link. And here's some text:

Climate scientists may have significantly underestimated the power of global warming from human-generated heat-trapping gases to shrink the cap of sea ice floating on the Arctic Ocean, according to a new study of polar trends.

The intergovernmental panel concluded that if emissions of heat-trapping gases like carbon dioxide were not significantly reduced, the region could end up bereft of floating ice in summers sometime between 2050 and the early decades of the next century.

For the new study, Dr. Stroeve and others at the ice center reviewed nearly six decades of measurements by ships, airplanes and satellites estimating the maximum and minimum area of Arctic sea ice, which typically expands most in March and shrinks most in September.

Dr. Stroeve’s team found that since 1953 the area of sea ice in September has declined at an average rate of 7.8 percent per decade. Computer climate simulations of the same period had an average rate of ice loss of 2.5 percent per decade.

Yes, its just computer simulations, some may say. No! the opposite! computer suimulations were optimistic, and showed less ice loss than observed. I wish I had used my bike this morning to come here (although it would have taken the best part of the day to cycle a hundred km)

Finally, the End is Near for Pharma Reps

The NY Times reports on the malsane (for me) habit of big and small pharma to give away free samples to doctors. These samples are then passed to patients, often against suggested first line treatments. now, that's bad. It's also bad that pharma reps invite out for expensive dinner/lunches
doctors, with the pretext of talking them about the latest drug from their companies. I don't say this because my lady is a doctor and I am jaealous of the pharma shills knocking at her door. Well, that doesn't make them wellcome to me, for sure. I am an italian boy, after all. What really pisses me off is seeing all that money being spent in marketing ploys of doubtful effect on doctors. Money which the patients end up paying, at the end, with higher medicines costs, and therefore higher taxes. It's a lose-lose situation, excluded may be for pharma shills which, after all, have to eke out a living (and were more interested in driving a powerful free car than in doing actual science - stab!).

In the great scheme of things, probably, free samples do the least arm, I would say. As a child of a poor family, I have often been treated with free sample coming from my family doctor's cabinet. And, I am also OK with big pharma paying out conferences to doctors (and scientist, although the numbers involved aren't nearly the same - even as orders of magnitude) - but is it really necessary to run every single shitty medical conference at the Sheraton or Plaza? Isn't it enough to talk in the auditorium of some University, equally well equipped and certainly less expensive? I can't tell for sure, but hey, here's my two cents. If that is, doctors really are interested in hearing about the latest treatment, and not merely in getting a free paid holiday in a luxury hotel, all in.

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.

Yawn...

No work today. yet, I couldn't avoid waking up well before 7AM. Too much light around, I guess.

No cycling in the Ardennes either. My girlfriend had other plans, so I will tour this area, and stop-by the workplace to look for my mobile phone, who disappeared. last chance before going off to buy a new one. If I were to do, I'd try and get a smart one, with things such as real synchronising capabilities, and possibly a GPS, although this may make it quite heavy on the pocket. We'll see...

Since I'm free today, I'll try to finish off a post I started long time ago, on the reasons why I feel we need fundamental research. I don't even remember how and why it started, just came off some musing after reading something else.

On a side note, I may also try to read up the latest changes suggested by my supervisor to the never-ending thesis. And cntinue on reading my latest book, "The Wisdom of the Crowds" - may be I'll post about this one too, later on. Ciao!

I am GOOD!!! (well, I feel so)

Yeay, I've just finished attending/giving my six-monthly update to the interested people in the company about my work. It went easier than I thought, I surprised myself for my confidence with a laser pointer in my hand. I guess the tireless fortnightly exercises paid off, at the end.

Now, it's mainly matter to finish off the ongoing studies, write up final conclusions (especially on the evaluations of pKa predictors), and possibly make the merry round of consociate companies, showing off my skills and fishing for opportunities.

But from tomorrow, and for the next five days, it's holiday time! If I can manage to, tonight itself I'll head off to Anthisnes, tomorrow I'll wake up later than usual, and possibly cycle around the place. I am gonna love it. Then, Saturday I don't know, just relax with my lady, sunday back to bxl possibly for some more sunny cycling with allochtonous friends, then monday and tuesday of rest before starting again.

What would I want more from life?

And one day, those corals will be up in the sky...

I wonder what Disney's Nemo may think of it. The fish, not the vernian pirate-submariners.

So, Chris Rowan reports that a recent earthquake in the solomon islands caused the whole island to rise, some 3m in certain points so that now some corals are exposed at the top of small reefs. I mean, elevated reefs. Duh!



the picture above is quite telling uh?

Seeing this and following Chris words':

I wonder if you can find the remnants of reefs stranded by earlier earthquakes on Ranongga? By dating them and measuring how far they've been raised above sea-level, you could have a go at reconstructing the past seismic history of the subduction thrust.

I wonder of my own: Is it possible that one day these corals will be embedded in some mountain side? I mean, I don't know much of geology, but do the Himalayas contain fish fossils and such? Or they're heavily metamorphosed beyond recognition? Mah?

Presentation is done. Now, learn it by heart...

Ok, I am done writing the presentation. Unfortunately, owing to proprietary structures being shown in it, I can't post it around the globe, so you'll have to wait for when I'll be bored enough to actually start writing papers about my work. Ouch!

Now, the only thing is to learn it properly, difficult to do in the few hours left before the presentation, especially when the sun is shining like now and you've been closed in a room for a full week, fighting viruses and unruly data.

Unfortunately, I am not a natural like one of my colleagues, who just jump in front of the blackboard and can discuss coherently his own thoughts and work without stumbling and such. May be it depends from the fact that he actually reads his literature (and eats his veggies too), but hey, nobody is perfect! He didn't know of the existence of Antactica... So how's that, is the choice really between being a slacker in Pharmacokinetics or missing a whole continent? Can't there be a middle way? why do I find so much of scientific literature boring and uninspiring? may be I am just not cut for science. Notwithstanding the fact that I am one of the best person I know at presenting data in a graphical, novel and understandable way. Just, not good with words. As you can see for this boring blog...

Time to go now... See you soon! Keep reading me - if, I mean, you really don't have anything better to do - that is - talking with friends - or walking the dog. washing the dishes - or the clothes - hanging them - ironing them - including your pants - and your socks... and so on and on and on...

So, I have been volunteered...

So, I'm just back from the Tiger Mosquito's Weekly PostDoc Lunch, the self-organising open initiative for postdoc (buit also not) here at J&J Beerse, and I discover that I have been volunteered not once, but twice, for the third PostDoc Carnival, a run-around of (many, if not all) blogs written by postdocs...

Featured twice, in one of my romantic moods, then in one of my searches for aesthetics in science...

Anyway, I'm not a real post-doc, as I have to defend my thesis. yet. Actually, I have to complete writing first.

May be in the next four days of holidays. If it ain't sunny, and windy, in which case trying the new 1.80m wide kite takes priority. Kind of like this one. prettier (I hope, haven't broken the bag's seal yet).



Watch and learn, kids, this is how you do NOT become a real scientist!!!

And now, I'll chain myself back to the table, I fixed some new data and must find a way to finish off a powerpoint presentation detailing what I have done in the last six months, before I head off to present it tomorrow. Ow!

And oh, thanks to whoever inserted me in the loop ;-)

YES!!! I have made it!!!

I have beaten the flu!!! (well, ok, the cold and a sore throat) One day without shivering!!! And at the same time, I've managed to almost complete my assessment of pKa prediction softwares. Getting the results I was hoping for too ;-).

Not only, thanks to a fortuitus encounter in the loo I may go on and present my work in a small, but up and coming pharma which I already put my eyes onto.

Isn't this the second best day of my life? (second 'cause I hope the next one still has to come!)

Ciao from an euphoric Owl!!!

My Most Favorite Comics (II)

Nausicaa in the Valley of the Wind, a post-apocalyptic novel set in a far-away future, (some) thousands of years after humans devastated the planet, and a toxic jungle of fungi and moulds has taken over most of the dry land. A princess finds herself and her own valley in the middle of the struggle between the two largest empire-states over the control of the last invincible soldier, one of the bio-engineered robots who battled in the ten days of fire.

quite simply, one of the best ecological tale I've ever read.

My most favorite comics (I)

here's a comics that has a special place in my heart:

Ushio & Tora, la storia di un ragazzo (Ushio) e del suo rapporto nemici/amici con un demone a forma di tigre (Tora) che lui stesso libera dai sotterranei del tempio buddista di cui il padre sacerdote si occupa. Questo e' stato il primo manga che acquistai con l'intenzione di seguire, quasi x sbaglio. O forse no, e spiego dopo perche'. Ero in viaggio coi Boy Scouts x il campo estivo, e annoiato decisi di comprare uno di questi manghi di cui i miei colleghi all'uni parlavano. ken il Guerriero usciva al tempo su Z Compact, e il caso volle che proprio quel mese finisse x lasciare il posto a questa nuova serie di mostri, combattimenti, umorismo. Nello spazio di quei dieci giorni di campest lessi e rilessi il volumetto almeno tre o quattro volte. E non appena rientrato a casa, compresi che ero stato infettato dal virus. Un mese dopo l'altro, questo fu uno dei miei fumetti preferiti, ma il sogno fu interrotto bruscamente dal fallimento di Granata Press, pioniere del manga in Italia, al numero 14. Di cui io fui uno dei fortunati possessori, insieme al trasognato numero 23 (l'ultimo) di Nausicaa, ma questa e' un'altra storia).

Ritornando a Ushio & Tora, avrei dovuto aspettare varii anni affinche' i Kappa Boys, transfughi di Granata, riportassero il fumetto in Italia, anche se le nuove traduzioni, non piu' basate sull'adattamento americano, persero buona parte della verve che me le faceva adorare. Una traduzione letterale dal giapponese non sempre e' la scelta migliore. Vorrei scrivere molto di piu' su questo fumetto, ma ora non ho rpoprio il tempo. magari piu' avanti. ciao.

Yahii!!!

Jackie Chan plays StreetFighter (from the movie City Hunter, inspired by the comics by the same name)

A Masterpiece of Asian Advertisement

If it weren't for the subtitles I wouldn't understand a jota, and even like this I don't know where they are from - Somewhere between India and Armenia, I'd say.



But Oh they're funny!!!

Is google in the hands of creationists?

I was cleaning up my inbox, when I noticed a very weird "sponsored link" on my gmail:

the line says: "Intelligent Design - www.RealTruth.org - Controversy is Intensifying. Why is this issue so Divisive?"

you follow it, and find out that the piece is a somewhat ambiguous article about the Dover trial and a certain Behe. Nothing to worry about if it weren't for the undertones of the word, things such as:

"Why has this seemingly objective, measured disclaimer caused such a firestorm?" (referred to the Dover obligatory reading before teaching on evolution.

there's more:

"Predictably, some prominent media outlets are already framing this debate with a pro-evolution slant."

"Dr. Behe believes that he has faced considerable bias against his theory."

What a load of crud...

I tried to get rid of the websites in the settings of my webclips, but can't find it. Apparently Google, let me customise only my own addition, and the rest is for them to choose. depending on who shell out the money to be read, I guess. Well, as long as they don't start doing it on Google News. Not that I visit there very often. It's already rare that I finish what's to read for free on The NY Times.

Farm Bill is coming...

and Coturnix beat me to it. For those of you that, like me, didn't know how this US legal document influences the state of the whole world, have a read at the latest piece from Michael Pollan.

Must force my GF to stop night watches

Apparently, people who do night shifts live shorter than day-workers.

I caught the news from Coturnix.

Original is from an indian newspaper.

I am already pissed by the fact that Marie has to work during the weekend sometimes. On a very selfish basis, it completely ruins it for me too. 'cause I am fusional as she says, so I don't want to go out on my own. And even if I do so, I try to fit to her times, and this makes life very complicated. Without counting the fact that the following days are often sub-optimal too, since she's tired or else.

Aww, life sucks! Stop ranting and back to work now.

Bloody fever won't go down.

So, here I am, forced to work under the effect of paracetamol and stuff... my head feel stuffed, and I am envious of everybody else breathing freely and dressing liberally, whereas I am forced to wear wool, a scarf and still feel midly uncomfortable...

Yesterday fever spiked in the early afternoon, after some four hours spent in the office trying to advance this impossible pKa study.

Went home and ate some fruit salad and ice cream, all the while watching movies until my neck was to painful to stand there. Only then i relaised my fever was far too high, and had to force myself to the bed.

I finished watching "Deja Vu", which was quite OK for me. Excessively moral may be, with the whole "If you could change awful things that happened in the past, what would you do?" that Denzel washington hammer down the (sore) throat of the spectators. Whether they like it or not. The scientists, as usual, are portrayed as whimp, thnk god there's the good ol' cop to save the world and show them the right way to use the tools they created.

Other than that, the action is pretty solid. although why every american movie must end with a fist fight between the good and the bad guy is beyond me. pah.

I've also seen Lyrics and Musics, or the other way around, with hugh Grant and Drew Barrymore: Nice and warm, just right for a feverish guy watching movies on saturday night with his lady.

Wii would like to play...

Wii vs PS3

The GREAT cinema, as seen from Luna&Sole

So rude, yet so brilliantly comical...

I was afraid to post it for fear of being labeled as 'racist', but then I said, what the hell, I work every day with people from all over the world, my best colleague/friend is an indian, and I am pretty sure that if he could understand our dialect he would luagh at this too. Therefore, enjoy the mystical figure of the indian guru as seen from the low-thinking people of my city, Sassari.

I am in PAIN!!!

Two days spent fighting this awful sore throat, coughing congealed blood and whatever it is that clog my aerial ways, under blanket bombing of paracetamol and ibuprofene by Lt. Marie. Still, my neck pain hasn't gone away, and it's stopping me from working... well, not really, but it is making it more difficult, and it already is hard knowing that everybody in Belgium is out in the gorgeous sun... and I am stuck here, at work.

pants! hate it!!! Hopefully it will be gone by tomorrow... yeah, hopefully.

In the most powerful nation on Earth...

there's places where 11 out of a thousand babies die. And if you restrict to blacks, it's 17 out of 1000. This is to be compared with an US average of 6.9. Still, markedly higher than in Western Europe or the developed chunks of Asia.

check the table at http://www.infoplease.com/ipa/A0004393.html to get an idea.

I am sorry, but have nothing else meaningful to say.

YouTube anch'io!!!

I subscribed too.

username is gufodotto, as usual. will start voting, and uploading if I find anything interesting. see you there.

Li sindaci di sassari

Wonderful voice-over of my city council, where the phrases uttered have been modified to include previous mayors' names. It quickly escalates in a reenactment of a famous local song about the mayors of sassari and surrounding communes and their misfits.