Sunday, December 27, 2009

How to reach the Giga mark with plants




The 96-well microbiology plate and its plant analog?

New Phytologist recently had a commentary "From Galactic archeology to soil metagenomics – surfing on massive data streams" (New Phytologist (2010) 185: 343–348). It's an interesting, if not typical, update on Progress [with a capital "P"]. The comment discusses the large numbers of microbes in soils, the diversity of Operational Taxonomic Units, and the large number of sequences that can be read currently in a standard batch. Having worked tangentially with the new technology, it truly is breathtaking the amount of detail and volume of data that can be generated.

I used to think that the tradeoff between quantity and quality is a fundamental constraint in the world and it was especially acute in science. I'm not sure I think that any more. In some senses, quantity is quality--at least when it comes to scientific emphasis.

The amount of money that gets spent on new technologies in science is immense. Part of what drives where that money gets spent is perceived rates of Progress, but also just sheer numbers. It also helps to be able to collect data in the 10's of thousands, if not gigas or terras. Sophisticated data streams and analyses help.

For understanding plants, and definitely ecosystems, we have suffered from not being able to rapidly produce enough data. Pure and simple. Remote sensing data is weak, but we can generate a lot of it automatically. Same for microbial data. And genomics. Those things that we'd like to learn about, but we can't generate a lot of data, suffer at the macroscale when it comes to scientific investment.

One of the things that has been holding back plant work has been the scale at which we can generate data. It's too slow. We need to generate a lot of data fast.

96-well plates in microbiology are standard and provide a template for a number of processes. One thing that would help beginning to generate a lot of data would be to have the equivalent of the 96-well plates for plants. The similarity with 98-cell Conetainers is striking and makes me wonder whether it could become a standard. For example, there are roughly 2000 species of grass in the US. To grow one plant of each species would take about 20 trays, which is about 40 ft2, or the size of a standard growth chamber. A standard greenhouse might be 5000 ft2, which could house 2,500,000 cells, enough for 1000 replicates for every species of grass in the US, 250 replicates for every species of grass in the world, and 10 replicates for every species of plant in the world (assuming you could cram it into a tiny Conetainer). Collect one data point per cell and the numbers get big fast. A few data points and we hit the Giga mark in a month.

A standardized medium in each cell would provide comparable data, but one could also imagine a standard configuration of different soils to provide a spectrum of data, similar to the old Biolog plates. Soils could differ in nutrient availability or texture or salinity or origin. 98 cells gives you a lot of flexibility.

I wonder if in the plant world, we just haven't been thinking big enough. There are certainly logistical problems to overcome, but the giga mark is within reach. I just wonder why we don't do it.


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