Time to speed it up?

Picture this: a lab with one or more people huddled over well-aged stereo microscopes, staring intently into glass Petri dishes or small trays filled with a splash of water and marine sediment. They occasionally move sand grains and detritus aside with a needle and pick out microscopic organisms with fine tweezers, or suck them into a drawn-out glass pipette. They transfer them into different vials or onto microscope slides, and either make a tick mark on a sheet or hit a tally counter that’s standing off to the side. From time to time, one of them takes a pencil and makes a sketch of what they see under the scope, furtively looking back and forth between paper and eye piece, trying to get it just right. This goes on for days, weeks, months, years, decades… centuries. The faces change, the samples on the shelf get replenished faster than they can be worked up – the process stays the same.

Welcome to meiobenthology, the study of small invertebrates in sediments. This is how we’ve been working for centuries: we collect sediment samples using various types of grabs or coring devices, sieve the samples over different sized screens.. and then painstakingly pick out what we’re interested in. Methods and tools for processing sediment samples have not – or barely – changed. It’s probably one of the most time consuming tasks and surely must have a place among the scientific disciplines with the smallest, slowest data output – especially considering the vastness of the world’s oceans and the benthic habitat!

This tedious task is only made bearable by having good friends to chat with sit in the lab with you, by listening to the radio or music, and by intervals of going out on research cruises to get some more samples (and fresh air). And if you’re at least partly in charge of your own project, you may be able to think up some other analyses you can do to liven it up, analyses that require some pipetting, centrifuging, and general mixing of fun chemicals and sticking your samples into a big, shiny lab instrument that does a lot of the work for you.

Jenny Rohn has written about technological developments in health research. Dara described her own kind of tedium in a recent post. While oceanography is a truly interdisciplinary field that absorbs technologies and methodologies from all over the natural sciences, sorting sediment samples has not had the benefit of being made faster by a machine. The problem here is that so few people do it.

If the same development effort as in other areas went into this, we’d have the sediments from vast areas of the oceans classified and the biodiversity of the organisms it contains described in no time at all. It would also be immensely useful for environmental monitoring of estuarine and coastal areas, and palaeoceanography. There are attempts of automating the process; most are based on the concept of flow cytometry. In a quick, superficial search, I came up with two recent examples. Standardization of sampling protocols in coastal areas and the development of instrumentation are two of the aims of the NaGISA (Natural Geography In Shore Areas) project.

Of course, for unknown areas, there would have to be human sorting first, as it may contain new species which a machine would not recognize at first – or would it, if it got ‘taught’ the characteristics of all known species? Could it record the percentage difference in morphological features, and ‘tolerance levels’ adjusted or re-defined as species get described? Could morphological variability in some species be resolved and the identification of species in different labs/countries/continents standardized? Would this prevent groups of organisms in the same size range from being overlooked, as in the case of foraminifera, who often get overlooked when they’re in the same sample as metazoa?

Why is benthic biology and ecological research/monitoring important? The NaGISA website has a nice, concise summary:
Biodiversity can be used as a measure of ecosystem health and of biological interactions such as competition, disturbance, facilitation, predation, recruitment, and the productivity of a system. On a larger scale, biodiversity measurements can serve as indicators of the balance between speciation and extinction. Inventorying and monitoring biodiversity are crucial tasks for identifying and clarifying activities that impact ecosystems.

To me, biodiversity (and the documentation thereof) is one of the most urgent topics. This may sound pretty depressive, but in many respects, it is already past the 12th hour when it comes to inventorying our natural world, establishing current levels of biodiversity and documenting the richness of life today. Increased automation may be the only way to keep up or even just make a dent before things change beyond recognition.

Writing this entry, I came across this blog: “The Other 95% – An appreciation of the underappreciated majority of life”.

This post was first published on Nature Network, which has since been discontinued. The post has been moved to SciLogs, where you can also read the comments made at the time.

About steffi suhr

Once upon a time, I was an enthusiastic and hopeful biological oceanographer who did a bunch of work in the Antarctic. I was alternately wearing labcoats or extreme weather clothing and hard hats, but have long since swapped survival suits for dress suits and do science management, currently as the BioMedBridges project manager at the European Bioinformatics Institute. I still like to use my brain. I'm a German serial expat, currently - again - living in the UK.
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