Biosilico 2003

Thanks to the FI Center I was able to attend a conference at Stanford a little while ago called BIOSILICO 2003 organized by Scientific American.

It’s taken me a while to let the deluge of technical information and bioinformatics industry insider-jargon settle into a few themes that I can pull together. Over the next few days I’d like to recap the conference, not according to the agenda, but by what seem to be the indicators of developments in this important area of life science.

You might be thinking: What does this have to do with cancer? Well, the most frequently mentioned biological phenomenon at this conference was cancer. Everybody mentioned cancer, not so much the way a person with the disease would see it or even the way doctors think about it, but as the biggest challenge in life science—the Gordian knot of biology, if you will.

First theme: bioinformatics, the offspring of biology and information technology.

Perhaps a good place to start is with two definitions: bioinformatics and in silico biology.
The National Center for Biotechnology Information (NBIC) within the National Institutes of Health (NIH) says:

Bioinformatics is the field of science in which biology, computer science, and information technology merge into a single discipline. The ultimate goal of the field is to enable the discovery of new biological insights as well as to create a global perspective from which unifying principles in biology can be discerned.

So bioinformatics is the child of scientific efforts to study biology at a finer and finer level coupled with the technologies of ever advancing, computer-driven instruments and computer processing power. The most prominent exercise in bioinformatics to-date is the Human Genome Project (HGP). Earlier this year—coinciding with the 50th anniversary of publication of DNA structure by Watson and Crick—the final full sequence of a typical human genome (the total of the genes an organism has) was finished with all its 3,000,000 pairs of chemical components.

While many people don’t quite know what all that means, the figure 3 billion is an attention-getting number. The human genome is BIG. And the ability of the genome to be unraveled is testimony to great technological advances in automated gene sequencing machinery and in the ability to accommodate massive amounts of information coming in and being stashed in computer databases on a daily basis. Without real accomplishments in Internet communication and database design the HGP would likely still be puttering around on a limited scale and years from completion.

Then there’s the remarkable fact that the human genome is now available on the Web for the whole world to see, free. If you haven’t taken a look, I recommend it. For my money this is a modern wonder of the world, and it’s only a mouse click away.

The combination of improving machines and more massive computing power continues to be a dominant theme in bioinformatics. The field has moved on to map the genomes of other organisms, to look for genetic variations in populations of people, and to identify genetic expression variances in diseases including, of course, cancer. Bioinformatics now encompasses efforts to study proteins in detail, to try to understand how proteins fold and to predict folding, and to detail all the steps ‘twixt gene and protein. Then of course there are gene expression pathways, protein-protein interactions, etc., etc.

In other words, the amount of information needed to accomplish what’s suggested in the definition of bioinformatics above is vast. It’s mind-boggling to realize how much detail and intricacy there is in a single cell, something so small we can’t see them with the naked eye. But it’s there, it’s absolutely central to unraveling the mysteries of cancer, and bioinformatics is a discipline working to figure it out.

Now, looping back to definition #2: in silico biology. According to a drug development glossary, in silico biology is:

The use of computational algorithms to create virtual systems that emulate molecular pathways, entire cells, or more complex living systems.

Projects are underway to create computer models of cells and whole organisms. Computer models have had great success in designing computer chips, automobiles and even whole airplanes. The vision is to do the same thing with living things. If you had a good computer model of a human cell—and better yet, a human being—then figuring out impacts of therapies and drugs on would be much easier. Building such models in a kind of holy- grail for computer/biology visionaries. Reaching that goal is quite a ways off—some might argue it’s unattainable—but researchers are having a run at it. Not the least of their reasons is that drug companies would pay a king’s ransom for such a thing. There’s even one company, Gene Network Sciences, that has developed a partial in silico model of a colon cancer cell.

So basically BIOSILICO 2003 was an industry get-together on bioinformatics and in silico biology and, not insignificantly, the prospect of using these techniques to illuminate paths to dealing with complex diseases like cancer..

Next theme: The Data Tsunami