Gufodotto would like you to read these:

Saturday, May 26, 2007

Fly Me to the Moon

Here's a movie to keep an eye out for: Three young houseflies stow away aboard the Apollo 11 flight to the moon.

starring Nicollette Sheridan, aka Edie Britt in Desperate Housewives (I found this movie looking for other things about her, after I saw her committing suicide in the series). Sad, she was one of my favourite characters.

Friday, May 25, 2007

Technorati link up.

Technorati Profile

A World Without America

No, I am not advocating anything political, here.

I did some thinking, yesterday. I read some time ago this short tale (forgot by whom - may be stephen baxter?) where Europe wasn't there. it got removed by aliens during the sixties, to avoid an incipient nuclear war between USA and URSS. It isn't quite alternative history, such as in the years of rice and salt - the focus is on how this sudden removal, unnoticed by humans who have had their memories modified ad hoc by the creatures, affects the culture - for example, to explain the fact that americans, australians and south africans speak the same language, a theory of confluence emerges whereby all languages are thought to tend toward a form similar to english, with time. It's a nice divertissement, good for a short story but I somehow doubt it would hold for a full novel - like Asimov's Nightfall, which did suck when extended (by Silverberg).

Anyway, another interesting tale is A World of Difference by Harry turtledove, the current master of alternate reality, where Mars is replaced by an earth-like planet (Minerva) and humans get there and find life.

but what if another big discovery of our past had never been done? What if Colombo had never come back, and there never was any America? How would have the world shaped up? What if instead than America, they had found a different continent, inhabited by a more advanced culture, able to withstand the Europeans' rough game? Or what if Europe itself had been discovered?

So, my question is? Do you know of any book telling such a story? if so, please drop me a line. Thank you.

and googling I found out this: check out their forum, where you can actually post your Alternative Timeline. For example, a longer lasting Roman Empire, owing to caesar not being assasinated. Or a present where Brits rule Space.

The Boss of It All

Here's another movie, more low key, but which looks quite interesting to watch.

The NY Times describe it as "acidic corporate comedy" or , as "‘The Office’ Viewed Through the Looking Glass"

Have no time to detail now, but I'm really tempted to get hold of it... Never seen anything from Lars Von Trier - hopefully I'll get it in english rather than danish.

Again, Spiderman 3.

This movie was high in my expectations. I was looking forward to see Spidey (il ragnetto, as they call it in italian) in a black tight suit. And the sand-man did look gorgeous in the trailer. Yet, it seems destined to disappoint me. I am not a fan of the world's most favorite wall-crawler, by any stretch. Yet, sometimes it is nice to just sit down and relax, let your mind be transported in an alternative reality where you don't cringe at bad things. that was the sensation the Matrix gave me, until, that is, Morpheus pulled out a duracell and started bashing the laws of thermodynamics. That absolutely ruined it. Once again, is it that hard to pay some REAL writer with some scientific knowledge to draw these plots? I mean, it's not like there's any shortage of sci-fi writers, at the moment. Just look up Stephen baxter's or Greg Egan's number in the white pages, pick up the phone, and hey! presto!, a new sci-fi movie with guts and idea which would blow your mind away. But I realize this does not necessarily apply to comic book-inspired movies. They do not have to obey to those rules, being children of another media. So I was happy at watching the first Spidey, although the goblin sucks as an enemy. I just can't fathom why one would want to enclose himself in that kind of crappy metal suite, all while hovering in precarious equilibrium on that kind of flying SegWay. May be the Osborne father was an allegory of Dean Kamen? Who knows? Anyway, the other point that really ennoyed me was the matrix-style special effects. But enough with the old spidey.

A friend wrote me yesterday, to let me know that the third one really sucks. here are his words: una trama indecente, che sembra costruita con la tecnica del patchwork, ma di quello più marchiano, con il collage di tante storie insignificanti senza vero collante, insomma 2 ore e mezzo di puro niente...

which, once translated, sounds like: An indecent plot, built with like a patchwork, but a very low quality one, with no glue to keep the various stories together, meaningless when taken one-by-one. In conclusion 2 hours and a half of pure nothingness.

Now, it's only one person. but the most important thing is that we ususally don't like the same movies, so I think I'll go and see it. Cheers!

At World's End

Here it comes, the NY Times review of Pirates of Caribbeans' third installment, with a name vaguely reminiscent of Asimov to me (Star's End) - I didn't see the second yet, since I heard that the two were kind of collated together, like Matrix Reloaded and Matrix Reboot or whatever. Hopefully, the will not suck like those two. This one seems allright, with an 8.6 based on 1600 votes to date. even counting that those are fans, it can't be that bad.

Compared with Matrix, which went from 8.6 to 7 to 6.3. This franchise seems to be holding its grounds, starting at href="">8.0, then 7.4, and settling for 8.6 - which will probably change in the next few months, as votes from more people build up.

The Review is quite ambiguous, in fact, pointing out many good things, but also many more not so good ones, if not outright bad. I guess I'll see it anyway, once the two or three are in a watchable format on the pirate bay - Irony?
Or may be I will not, I have developed a kind of allergy toward Jonny Depp, since he was my ex's preferred actor. Silly I know, but that's life: I guess I didn't like him too much to start with. After all, she introduced me to Scrubs and I still watch it every week.

Study Finds Hurricanes Frequent in Some Cooler Periods

Ouch! even when the ocean has been warmer, in the past five thousand years, strings of hurricanes managed to ravage the Atlantic Caribbean... This is the conclusion of some analysis performed by some scientists at the Woods Hole Oceanographic Institution. Here's their press release. Apparently, variation on the intensity of El Niño and monsoon intensity in West Africa influence the Caribbean hurricane season.
Should we trust them? Are we sure they are not some kind of fake research institute funded by republicans? As a matter of fact they're not, and they state their position on real warming quite clearly in the paper, saying that more than one mechanism may be at play in determining the weather patterns in the area - Global warming effect seems to be ascertained, and if it were to compound with one of these cold-pacific, rainy-Africa periods, effects might be even more devastating than expected. No Hurray for global warmers denialist, then. Quite the opposite. But then they will probably laugh at the idea that one can obtain reliable sampling of past hurricane intensity from the muddy bottom of lagoons. Their intelligence, unfortunately, can't grasp that much. In the mud, they simply live...

a funny news from their website: Vitamin B12 Is Also an Essential Vitamin for Marine Life
The vitamin has impacts on the marine food web and Earth’s climate - reading it like this, it looks like we should dissolve big-ass pills of vitamins in the oceans, to keep it healthy. But don't worry, those scientist haven't gone mad...

in the words of the authors: The presence or absence of B12 in the ocean plays a vital and previously overlooked role in determining where, how much, and what kinds of microscopic algae (called phytoplankton) will bloom in the sea, according to a study published in the May issue of the journal Limnology and Oceanography.

These photosynthesizing plants, in turn, have a critical impact on Earth’s climate: They draw huge amounts of carbon dioxide, a greenhouse gas, from the air, incorporating carbon into their bodies. When they die or are eaten, carbon is transferred to the ocean depths, where it cannot re-enter the atmosphere.

Many more news to discover in their website... go and check it out!

Thursday, May 24, 2007

Chimera, Grifon, Laelaps...

Which one is NOT a mythical creature?

Laelaps introduces us a really intelligent alternative to visiting the Creation Museum, some damn piece of crap put up by some pice of crap-ass creationist in the american untellectual junkyard.

So, you should rather go, Laelaps suggests, to the American Museum of Natural History's exhibition on Mythical Creatures, where fantasy is certainly better used than in thos bible stories - I think desert shepherd should have been just that, without attempting to compete with science fiction with their "Bible".

(I will admit though that I read the bible in comic version, where I was a child - it was given to me by a nun aunt, and I didn't know better. drawings were ok, too, although I found the stories strangely anticlimatics. Also, I believe the Apocalyps wasn't include. The only decent part, probably. Pity.

Luckily, I have the Gaiman and Pratchett version of it.

Kate, I hate you!!!

How could you possibly throw mud on my idols? how do you dare to put dinosaurs' purity and chastity in discussion? I know you're just pointing at words uttered by someone else, but shame on you for propagating such infamous lies!!!

[irony hat off] now, I can enjoy reading the discussion itself. thanks a lot for showing me the light...

I guess this picture may be interpreted as a carnosaur leaving a love byte on another?

Gay couple steal child!!!

Do not worry, I am just kidding.

It's just couples of Gay flamingos, as reported by Kate Hudson at Secret Sex Lives of Animals.

Apparently, this particular couple had been desperate to start a family, like many human gay couples. So, they did adopt a children who was left on its own (I don't know whether abandoned, or orphaned). And it doesn't seem to be uncommon either. many male flamingos pair up with other males, apparently 'cause there's an imbalance in the sexes (opposite to that in human - I am happy I am not a flamingo - that would sucks) so they have to. And sometimes may be they just can't get along with females. I am sorry I have my troubles with mine too, from time to time, still I'd rather stick with her. Actually, in one week we'll be living together! Hurrah!

but, back to gay flamingos. I wonder whether there's example of lesbian couples in nature. I've never heard about them... :-?

Google's User Experience Research

I signed up to complete Google's User Experience Research. The banner said something like "Would you like to play around with blogger for one hour or so, and get 100$?"

Of course I want. At the heart, I am still a student, happy to drop down a pill even if it makes my hair falls (that's NOT how I lost them - long story) - so, money for toying with computers? that's MY current job, right? why not moonlight?

Hopefully, they will not ask too much about my personal life.

Until now, it's mostly about the usage of their web services - most of which I enjoy, some other I rarely use, a couple I don't know what they're about - Orkut? what's that?

Third page of five: usage of Google's and third party softwares and online services, for communication, news reading and such.

Fourth page, more of the same.

Fifth page, is for employers, so just skip it.


page says: Thank you for filling out our survey. We will keep your details on file and contact you when a suitable study comes up.

So, where's my money? What? that was the application form? You bastards!!!

Learning Neerlandese

Ik studeer graag nederlands, maar het is niet gemakkelik. Which means: I like to study flemish, but isn't easy.

Not at all.
Yes, I had my first dutch lesson today. Its hard, but not too much in fact. few rules, and lots of exceptions... Pronunciation is easy for italians, since only 'g' is pronounced a kind of guttural 'hgh'.

We'll see how I fare on the next les(sons)! for the moment GooieAvond.

Flops at the user group meeting

I've at the end, decided to decline the invitation to go up and speak at the next ChemAxon Users' Group Meeting.

It was enticing the idea of having been invited, although I do not hide to myself that they did so because they suddenly had one cancelation. Still, it's nice to know they thought of me.

But, I went for a decline. Too many things to do in the next few days, I did not feel like
adding one on top of the move, and most importantly the presentation in TiboTec. That one, could really get me a job. Plus, my mentor kind of suggested that I may get the opportunity of presenting my CV work, if she manages to avoid it. Finger crossed for bot. Now, that I would really like. Plus, it's certainly more scientifically interesting than showing a benchmark of badly performing softwares.

Hopefully, everything will coagulate nicely, in a big omelette which I will devour piece by piece in the next few weeks. Eggs, breadcrumbs, cheese, parsley and all the rest :-)

Just in case you were wandering who I work for, here it is: Janssen Pharmaceutica

Tops at the Box Office

Tops at the Box Office

1 Shrek the Third
2 Spider-Man 3
3 28 Weeks Later
4 Georgia Rule
5 Disturbia
Here's a cut and paste of todays' tops at the box office from the IMDB

My Drug Development Training

Quite interesting training, yesterday...

A full day listening to the hypothetical structure of a drug development pipeline... from Discovery to Early Development, through the Clinical trials (I, IIa/b, IIIa/b), 'til Marketing and Post-Launch Follow-Up (often called Phase IV Trials).

Quite interesting, mostly for the comments of people who worked in one part or the other of said line... Noteworthy, a german guy who pointed out how actually very few, if any, drugs ever come out from the pipeline where expected, since often unexpected side effects open up new therapeutic possibilities for that molecules, and the original reason for developing it goes in the waste bin for one reason or another - extreme example is thalidomide, infamous drug retired from the market 'cause of its teratogenicity (is this the right word?) now enjoying a second life as therapy fornewly diagnosed multiple myeloma (don't ask me too much - check it on wikipedia).

I had my quibbles about the fact that the part on drug discovery and early development was presented, not explained, so that many of the non-technical people were left with doubts. What's the use iof just reading a definition of Half-life, or explaining what ADME means if then you don't explain what we actuially mean by the various ophases, particularly Distribution and Methabolism, the most esoteric for a non initiated? Yet, may be I am too harsh. I think I am not.

The last part, delivered by a marketeer, was very interesting, if a bit rushed out. I never thought that marketing did enter drug design since the very first phases o discovery, when they gently steer the research toward easily marketable and proficuous drugs. It certainly makes sense, just I never though of it.

That's it. food was good, and free, plus some ladies were worth looking at :-)

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.

Wednesday, May 23, 2007

My presentation Training

I feel like JD in Scrubs today, with an inner voice following my own life, and frequent digressions in alternative realities...

Anyway, yesterday I had a very pleasant training experience: presentation skillz, something I felt I badly needed, although I have been definitely getting better in the past months (words of my bosses and mentors, not mine).

Still, the training was scheduled so there I went. nice to have patisserie in the morning as second breakfast...

and the talk was nice, delivered by a motherly south-african teacher with the kind of positive attitude everybody hopes to have when presenting his own story to an audience.

Not many tricks learned, in fact, more of general theory on how to grab but most importantly keep the attention of the spectators. It wasn't easy to follow, at times, since pretty girls were all around and I am easily distracted by cleavages (pig!)

At the end of the day, the moment most feared, an improvised presentation on a topic of our choice to the whole group, foloowed by real questions(!) and judgement on our style...

I was initially planning to present a tiny bit of my work, but then thought what the hell, everybody is going to do that and it would be boring, so I went for something completely different:

How (and why) to download movies and music form the internet (for free).

I actually insert two attention grabber right at the begin, back to back.

I first did ask "How many of you did ever download one mp3 from the internet?"

then I gave her a piece of (made-up, but realistic) statistic: 75% of the Internet Traffic is composed of peer-to-peer exchange (concept illustrated by a pie chart)

The whole lecture was structured following cartoons and hand-drawn (by me, yes) piccies, with me talking over them...

They did like,it, oh yeah... may be I'll get the chance to scan the piccie and post them up here...

Now I am off for another seminar, this time on the various processes of Drug Development...

See you soon!

Tuesday, May 22, 2007

Everybody stand back...

A different James Bond

Deinosuchus (aka Giant crocodile from the far past)

Quick, everybody go and look at Laelaps post on Deinosuchus.

Here's what wikipedia has to say about this big, big, big crocodile.

And here's what it shows:

Image below is drawn from the "Prehistoric Park" series, from Impossible Pictures - the place where Darren Naish now works. It's not deinosuchus but it was too juicy not to link it.

So, how's Shrek the Third?

Judging from the IMDB, the chicken isn't making golden eggs any more... I guess the character are getting tired and don't have that much to tell... here's what the NY Times has to say:

For all I know, there may be an endless supply of “Shrek” sequels in the pipeline. That DreamWorks ogre’s skin is the color of money after all. But there is nonetheless a feeling of finality about “Shrek the Third”, a sense that the tale has at last reached a state of completion. it goes on about the character reaching maturity and entering fatherhood, and so on...

Still, the popular vote is clear, with imdb scores decreasing from 8 (Shrek 100K+ votes) to 7.7 (Shrek II - 50k+) to 6.9 (3k+). Even accounting for the fact that early viewers may be hard core fans, and therefore harsher judges... the drop is severe and I don't think it will be recovered. Quite simply, the franchise has lost its allure. Even the fact that less people bothered to vote for the second is witness to this.

Well, as usual I doubt I will have time to go and see it in the theater, hence I will wait for a decent dvd rip to pop up on the net (ever heard of aXXo?) - and enjoy one of those boring fall afternoons.

See ya!

Light Blogging today

I am full-time into a seminar on how to improve my presentation skiilz.

Tomorrow, same thing, I'll have to attend one on the general layout of drug development: hopefully it will be general and not tied too much to my company only. Well, not 'mine', the one I work for.

fter that it will be ablur to reach the end of the week with some work done and some stuff already packed in the house before the big three-days move experience. Gawrsh!!!

Monday, May 21, 2007

Evangelion!!! Live Action!!!

The greatest of Gainax successes becomes a live action movie.

I just hope they get the chance to properly do the effects, as the one shown in this trailer do suck a little.

update: new trailer: it sucks even more. they didn't even get the taglines right. "A boy has to decideD" "The destiny of THE Humanity", oh yeah, that would be Humankind... never mind - have a look yourself.

And what's with the freaking american accent of Kusanagi? I hate Americans for being so self-centric (not that japs aren't when they set all the ultimate fortresses of humanity in their own little island (less than 1% of Erath surface, yet statistically unlucky to incredible levels.

AND - apparently is an easter egg. or fan art. in the case, they did a decent job.

Wings of Honneamise

First movie of Gainax. A very realistic telling of a space program in an alternative reality.

Slow, yet one of my favourite anime


Some of the best explosion scenes froma collection of anime - I recognise most of the m - how geek am I?

New Piccie of the Month

Look at your right! I changed in advance the piccie of the month. as a bonus, and because I am not sure I will have that much time to post around in the following days, with all the busy things. seminars at work, move to mechelen and such.

Anyway, here is the elephant rock, a natural monument of my beautiful island. carved by wind and... more wind, I'd guess. actually, I don't think so, as it isn't smooth as wind-carved rock usually are.

You can find it here: It's the little dark spot at the center of the picture, just outside the road.

In the picture, you can also see my dear lady stretching up to reach the rock... almost there, but not quite. ;-)

And I'd believe it too!

I mean, I would believe it if the guy in black were to specify that the Space God was nothing less than the "Flying Spaghetti Monster"

Of course, the two turtles were hurled down, slammed together, their feet jammed, and voila`, here's planet Earth! Spherical as observed experimentally.

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.

Sunday, May 20, 2007

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!