Recently, Jonathan Eisen at UC Davis tweeted a comment made by a structural biologist at the 18th Annual International Meeting on Microbioal Genomics in California. The comment was along this line “if you don’t study purified enzymes in tube it isn’t science”. Although I understand what the structural biologist meant, I was shocked to hear that type of comment in 2010.

Unfortunately, the heated debate between “experimentalists” and bioinformaticians is far from being over. In a nutshell, the biology world can be roughly divided into 3 worlds. The experimentalists doing only wet biology occupy the first category. They trust only what is inside an Eppendorf tube. At the opposite, we found the second category: the bioinformatics world. The bioinformaticians put into equations what the experimentalists found. Then the bioinformaticians try to understand, and model with an ever-increasing accuracy any biological elements. Their work can be a genomic analysis or predicting the 3D structure of a protein among others. The third category of scientist sits in the middle. They believe that using both wet and dry biology is the right combo to better understand everything.

A fringe of hardcore experimentalist does not believe in all the bioinformatics tools and their power to answer some fundamental questions. Of course, that leads to endless debates amongst scientists. *Yawn* The main argument of experimentalists is “A computer program can’t explain or predict a biological phenomena because there are too many unknowns. If you don’t do wet biology/biochemistry in a tube, it isn’t science. ” Well…sure…Last time I checked, there is a descent number of BS analysis coming from experimentalists. Right? Also, there are numbers of wrong analysis using only bioinformatics too. *Facepalm right here*

As for myself, I am a strong advocate of using the best of both worlds. For instance in structural biology, an X-ray structure gives an accurate snapshot of a 3D structure…but that’s it. What about the flexibility during functions? What about the domain motions? How to accurately understand the mechanism of an enzyme? How does the substrate enter the active site? How the product leaves? How does a protein interact with a partner?

There is a huge gap between the world of known structures and the universe of known protein sequences. Structural genomic projects are unable to keep up with newly discovered genes. How to accurately gain access to nearly all of the 3D protein structure of the whole proteome? Those are just few questions among many more.

Bioinformatics offer many great tools to answers all those questions as long as they are properly used and validated. Unfortunately, some scientists don’t agree with that.  Well! This is 2010, people. It is time to embrace the 30+ years of steady developments in both computer science and bioinformatics and to apply them to biology, broadly define. In science, most of the “easy” stuff has been already unravel. What is left? More difficult and complex problems. In order to make significant contributions in Science, one has to cross boundaries with mixed methods approach. Inter-disciplinary is the way to go!

Over the last months, I have been monitoring in disbelief the number of “comments-spams ” that hit my website: 4,464 since March 23. Too me, it is way too many for a website that gets an average of 10 legitimate visits per days. I absolutely can’t wrap my mind around the fact that somewhere an army of bots/zombie PC are burning a lot of CPU and bandwidth to vomit a load of nonsense comments on websites…Thankfully, the spam gets caught in powerful filters such as Akismet. So far 99.955% of the comments are junk on my site…It leads to the question: “How much energy can we save if we take down all the spam-servers?, how much bandwidth can we save?