Skip to main content

Beyond Genome Dips Into Theoretical, Practical Future of Biology

SAN DIEGO, June 19 - The Beyond Genome conference, scheduled at the San Diego Civic Center this week between the international reptile breeders show and a "scrapbook expo," didn't bite and gave the 600 or so participants more than a few mementos to add to their files or use.

 

The conference included four tracks, RNAi and bioinformatics the first two days; and systems biology and proteomics the third and fourth day, along with exhibits from a small selection of vendors. The RNAi track was easily the most popular, and some sessions were standing room only as speakers and participants sought to clear away some of the fog that still surrounds this new and exploding technology.

 

"We don't really understand the why yet, but our data tells us it's different," said Xu Ren of Amgen, speaking of the discovery that the sequences in a gene that work as effective targets for siRNAs are different than those that work for antisense. But Ren might as well have been speaking of the field in general. One reappearing question was the issue of off-target effects -- if, when, and why it occurs, and how to avoid it. Others discussed optimum concentrations of RNAi to introduce into a cell; ways that siRNA can be modified to become more stable; delivery vectors and techniques; and how to reliably quantify results. (For a more detailed report, see Friday's RNAi Roundup.)

 

In bioinformatics, gene-expression analysis remained a dominant theme, joined by talks about data integration as well as protein informatics. Atul Butte of Harvard, who spoke about the use of signal processing and other techniques to generate gene network hypotheses, complained that he was "a little bit annoyed about the field of bioinformatics" lately, showing a slide of the book Bioinformatics for Dummies. (Yes, it's a real book.) "I want to talk about how to get us out of this 'dummy' mentality," he said, noting that algorithms other than basic clustering have to be employed to build networks between genes.

 

In another bioinformatics talk that was definitely not for dummies, Brian Moldover of Aventis described computational tools to analyze alternative splicing in order to find novel drug targets not already covered by patents.  

 

Several participants in the bioinformatics track from a major pharmaceutical company said they learned more about various databases and tools, and took away valuable hints on how to better and more efficiently exploit their computational resources.

 

While many participants said they just came for RNAi, a good proportion stayed on for the second half.

 

The proteomics track focused on biomarker discovery and protein informatics, while the systems biology sessions included innovative talks such as one in which Harverd Sauro, of the Keck Graduate Institute, showed how electrical circuits -- in particular a feeback circuit -- could be used as models for understanding biological systems, in particular a MAP Kinase cascade. "Biology is looking more and more like an engineering discipline," he told GenomeWeb. "Or perhaps, it is really reverse engineering."

 

Sauro's teacher, Cal Tech researcher John Doyle, gave a keynote address in which he explored this reverse engineering further, demonstrating how all advanced technologies, including cells, can be mapped into these "bowtie patterns" with a heterogeneity of inputs, a reduction, at the middle of the bowtie, to basic building blocks (catalysis), then a building up from these blocks to more complexity and heterogeneity (biosynthesis.)

 

Doyle also discussed the urgent need to further develop this overarching theory of biology, in order to move computational systems biology forward and better organize the daunting complexity of the field.  A significant obstacle to developing this large-scale theoretical infrastructure, Doyle said, is what he called "the tower of babel." "You have a thousand screaming monkeys with their own view on how things should be done." Another problem, he added, is that the people who are really qualified to solve the big problems of theoretical biology, are working on the internet or advanced technological systems, where the rewards are much greater. But this is just a transition period, he said. "In the long run, [theoretical] biology is going to be a great area."

The Scan

US Supports Patent Waivers

NPR reports that the Biden Administration has announced its support for waiving intellectual property protections for SARS-CoV-2 vaccines.

Vaccines Versus Variants

Two studies find the Pfizer-BioNTech SARS-CoV-2 vaccine to be effective against viral variants, and Moderna reports on booster shots to combat variants.

CRISPR for What Ails You

The Wall Street Journal writes that CRISPR-based therapies could someday be used to treat common conditions like heart attacks.

Nature Papers Review Integration of Single-Cell Assay Data, Present Approach to Detect Rare Variants

In Nature this week: review of ways to integrate data from single-cell assays, and more.