Friday, May 30, 2008

So...what is going to happen to them?

Selling the war selling a book. Ouch!

Please forgive me, this has absolutely nothing to do with biology and I know I am not very original with this posting but this is just too funny....Am I dreaming?

If you want more of this comedy, you can read the transcript of an interview Scott McClellan had with Anderson Cooper. He is a real master of spin, he was hired by W. for this specific talent!

In all fairness, I added the next video where McClellan has a chance to explain his book and views to Katie Couric

Peru and the economy of bird poop

Guano is a great mix and there is a market for it, once again. So what the heck is guano? After all, even Captain Haddock, a seasoned sailor did not know what it was (See Tintin, Prisoners of the Sun). Could it be the latest coffee fad from Starbucks? Not really! While the phrase "I would like a Tall Guano Latté to go" might sound realistic, it is quite unlikely that guano will end up in your favorite beverage! This term is used in Peru to differentiate between useless bird waste and the nutrient-rich waste of cormorants, pelicans among others. Guano is dung!

Now that you are aware of that fact lets see what is the hype about this complex substance. Guano, especially Peruvian guano is very rich in phosphorus and nitrogen in the form of ammonia. Before synthetic fertilizers were made available, natural sources were an important part of the economy of producing countries including Peru. Peruvian even fought with Spain to preserve it during the so-called "guano boom" in the 19th century. Starting in 1840 and for 30 years, 12 million tons were exported to America and Europe and then the "guano boom" busted.

Today, soaring prices for synthetic fertilizers ($600/ton last year) are rejuvenating the demand for guano and the Peruvian Island Isla de Asia has plenty of it....well not as much as before, but at least enough to sustain a 10 to 20-year demand. Peru exports it guano to Israel, France and The United States at a price close to $500/ton. The problem is that it is not a sustainable source because that the bird population is declining. The numbers have declined substantially from what it was in the 19th century (60 million birds compared to 4 million today). The seabird population is declining because of overfishing....because you see seabirds live on fish and guano, to be produced, needs food to be digested by someone....good Peruvian guano might not be around for very long.

NY Times
Click here to access a great slideshow

Thursday, May 29, 2008

Physics rules the world

One of my college professor used to tell us that physics was the MOST important science to understand life because all the other ones rely on physical concepts. I did not like physics too much and decided to pursue a career involving biology. Soon enough I realized that physics was indeed at the core of almost everything. From the aqueous solutions to the cell membrane physics define what really happens.

Protein folding is no exception. Physical forces influence the interaction of thousands of atoms and shape polypeptides. No function! The problem with a physical approach to understand and model protein folding resides in the fact that femtosecond calculations have to be made. As Ken Dill (UCSF) puts it, it is all about timing:

"You need to be faithful to the atomic dynamics from one instant to the next, otherwise you violate Newton's laws"

Kenneth Dill is part of a group that participated in a protein-folding competition: CASP7 (Critical Assessment of Techniques for Protein Structure Prediction) held in november 2006 in California (Pacific Grove). Basically, each team (there were 250 teams) had to predict the structure of 6 three months! To do so, many, including Dill, used supercomputers such as Tungsten at NCSA. To predict protein folding, Dill and his group used the ZAM model (Zip And Assembly), once a few amino acids find their position, the rest of the amino acids in the polypeptide interact with each other in a Zipper fashion.

Fig 1: ZAM predictions in CASP7 compared with experimental PDB structures. The GDT (CASP's Global Distance Test) gives the percentage of residues (x-axis) whose alpha carbon coordinates lie within a given cutoff distance (y-axis) from the native structure, for predictions by all participants in CASP7 (orange colors). The best predictions correspond to lines in the lower-right quadrant of the graph. The five ZAM models are shown for each target in gray, with the best model highlighted in red. (click here to access original Website)

The physical approach allowed adequate prediction for 4 of the 6 proteins (see figure 1) and Dill thinks his group did at least as good, if not better, that other groups using bioinformatics.

Yes...I have to admit, physics still has a very bright future!

For a list of NCSA projects click HERE

Image source:


Stats in real time. Anything wrong with this picture?

SHAGYA BLOG: British Columbia Government Attacks Freedom of Speech

SHAGYA BLOG: British Columbia Government Attacks Freedom of Speech

W.A.C. Bennett, Gordon Campbell and the end of a dream

I am new to the West Coast and I hope I never lose my constant amazement about the natural wonders of British Columbia and the quality of life here. But this could change.

The BC government is now selling rivers to private companies so that they can produce cheap electricity they will sell at a high price. This is exactly what W.A.C. Bennett did...but in reverse! Bennett, a former BC premier, brought power generation and electricity production to the people of BC. The Campbell government is now reversing the tide....a very interesting video can be found HERE

Not surprizingly, they also slashed the budgets of post-secondary institutions. A pro-business government? You better believe it! Oh...before I forget, Gordon Campbell's new election gag law imposes extreme limits on any organization who wants to talk about many topics from December of this year until the May, 2009 provincial election. What are these topics? Here is a list just fro you (from the Just Shut Up BC website)

  • Climate change, health care, public schools, the Olympics, child care, transit, fish farms,affordable housing, run of river private power projects, carbon taxes, raw log exports,resource-dependent communities, public private partnerships, minimum wage, free trade, mental health services, offshore oil drilling, public power, electoral reform, the gateway project, post-secondary education, taxes, clean air, First Nations treaties, public safety, seniors’ care, harm reduction, poverty...and more
Other blog interested in this topic:

How to become a genius

Being a genius has a lot to do with perception...either you perceive yourself as a genius and nobody else does or you think you are just a regular person and everybody thinks you are a genius. Sometimes you might be a real genius and everybody knows it, including you...but that is quite rare. It seems there are ways to "become" a genius and it has little to do with a gift from mother Nature (or God for that matter) rather than being able, or lucky enough, to "see" something nobody else saw or even bothered looking at.

Here is a paper published in PLOS Computational Biology that just might help you. I decided to bring the highlights to on genius....

1) Nobody cares about your age, especially if you are young and, it gets even better....if you are a "nobody", nobody really cares. You can imagine very controversial concepts and maybe you will be lucky enough (and smart enough) to be right on target. The most important thing is to keep your mind open to new ideas and concepts....people once thought planet Earth was flat!

2) Look out for the weird....something unusual happens? You can do two can trash the results that would screw up your error bars or you can try to replicate these "weird"result. By the way, if you need to refresh your statistical knowledge, the Bayblab guys have something for you.

"This should be encouraging news for those of us who don't consider ourselves geniuses. The best way to promote scientific success may be to maximize exposure to chance occurrence and events—especially those that have more upside than downside potential. So, don't just ignore those little inconsistencies that arise in your work, give them some room for consideration. This is something anyone can do, though it takes time and courage"

3) Take risks....ah...risks! Calculated risks maybe but risks are an important part of it. I suggest you buy a Magic 8 Ball if you are too scared. Chances are you will come up with news ways of analysing the situation!

4)Enjoy your work....nuf said!

5) Learn to say NO!...that is difficult. Here is a way to look at it: Saying NO is actually saying YES to other things! Ah...logic!

6) Learn the joy of writing and presenting. Open an account on Blogger and try to say things that make you look like a genius....Expose your ideas to other ones. CONFRONTATION!!!! Eventually, you will have to present something, so remember that practice makes perfect...just like your mother tells you (or used to tell you)

7) See the big picture. You are going somewhere with this new concept...right? Remember and, most importantly, understand the WHY...WHY is this important, WHY should someone listen to you for more than 5 minutes (or 5 seconds)...WHY????

You are now on your way to become the very best scientist this planet ever had.

Giddings MC (2008) On the Process of Becoming a Great Scientist. PLoS Comput Biol 4(2): e33. doi:10.1371/journal.pcbi.0040033

Wednesday, May 28, 2008

Seen in Port Angeles, WA

Of course I was expecting exceptions....To us, Canadians, that seems out of this world!

Should we be surprized?

Found PLOS Biology

"Community pressures place significant stress on teachers as they try to teach evolution, stresses that can lead them to de-emphasize, downplay,or ignore the topic."

Panties, superstition and Myanmar

I was reading this on Radio-Canada's website today...interesting. Very briefly, this SITE ask women to send their panties to the Myanmar ambassador in Ottawa.
WHY? Because, according to a popular belief, men lose all power when they touch a piece of feminine garment that was worn under the belt...especially panties. Ladies, get rid of these old underwear for a good cause.....

Image source:

Scratch my back and I'll scratch yours

An editorial published today in PLOS medicine brought to light something many of us (read "science literate") already know. "GOOD news", especially medical "GOOD news", come with a price tag.

Medical good news are fabulous because most are concerned about health-related issues. To no surprise, when a medical breakthrough is released we listen and watch, almost captive. When these news are "sponsored" without our own knowledge this becomes a problem. Why? Simply because the public is generally uninformed (or misinformed) about their own bodies and the alternatives presented through these "GOOD news" seem to be the only ones because the sponsor, usually a big pharma company, pays for a powerful release in prime time TV. These, folks, are not news...they are advertisement!

Image source:

Tuesday, May 27, 2008

See the big picture?

I had this idea on a smaller scale and not as an autoportrait....argh! Got to fire up the right side of my brain! Creativity man...creativity!

See for HERE!

PS: Not the most eco-friendly art on the planet.....hummm!

Let's get serious!

LOOK !!!

I do not normally post political things but I recently read: "London has 10,000 crime-fighting CCTV cameras which cost £200 million...". This makes me think in biological terms.

You are being watched, you adapt....but you can't watch the watchers

Some become creative....a niche for everyone! Wonderful world!


Friday, May 23, 2008

Human 2.0 Olympics

Oscar Pistorius is a double-amputee South African athlete. I admire anyone that rises above life's challenges. I admire anyone that becomes a model for others. I admire anyone that decides they can do anything they want to. I really do! Oscar Pistorius is one of these humans that decides an obstacle is just obstacle! I admire that! So much, you have no idea.

Despite this admiration I could only agree with The International Association of Athletics Federations (IAAF) decision to not allow him to compete in the Olympics. I really think his prosthetics give him an unfair advantage over the other athletes. Although I agree with that decision, I find it quite ironic that he has an "unfair" advantage....interesting when you think many of these athletes are using performance-enhancing much for fairness!

This decision was overturned by the The Court of Arbitration for Sport (CAS). I think this is a mistake and lack of courage from the CAS. How far will that go? The door is now open to Human 2.0 Olympics where genetically-modified cyborgs will compete. The Olympics will now become an ideal that is even farther than it ever was before for kids.

To get a spot on the start line in Beijing, Pistorius has to qualify but many doubt he will make it, apparently he is not in the shape he should be for that ultimate racing exerience. This does not matter wheter he makes it or not....the damage is done!

Also published on my other blog:

Tuesday, May 13, 2008

Reach out!