Life strikes back – harnessing genomics to understand and value biodiversity

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Edited notes from Research Tuesday public lecture 8th May 2012

It still seems amazing to me that we don’t really know how many species there are on earth. In a famous study conducted in Panama in the 1980s, rainforest trees were ‘fogged’‚ insecticide sprayed into the canopy to kill all the life that is harboured in them, and then classify the resulting rain of dead insects. A total of 1,200 species of beetles alone were collected, 80% of them unknown. This is unsurprising as our estimates of life on earth have vacillated wildly between 2 and 100 million. Only last year our best estimate was 8.5 million, but since then the number of fungi has been revised upwards by 300%, giving us a current best estimate of just over 12 million.

Of all these millions of species, we have described only approximately 1.4 million. We have done this over the last 250 years using a classification or “taxonomic” system developed by Carl Linneas. For those of you without a calculator, this equates to half a million species a century, and at this rate it will take 2000 years to complete the task of naming all life on earth.

There are more than a few problems with this timeline. Principally that we are now living in the anthropocene, an identified period of the earth which is seeing large numbers of ecosystems wiped out and species sent to extinction by human activities; habitat clearance, introduction of invasive species and climate change.

In fact the rate of extinction today is estimated to be at its highest annual rate in the history of the earth. We risk a large proportion of species shuffling off this mortal coil before we even know they exist.

Given the myriad of concerns in the world today, why should we care about the brief lives of fungus or sap sucking bugs? Because we cannot sustainably manage biological systems without knowing the basic building blocks, and we may inadvertently destroy the critical, but currently invisible, threads that hold our ecosystems and foodwebs together. You cannot place a value on the unknown, so we must work towards greater knowledge, and do it faster.

Fortunately our penchant for technology, in the shape of genomics, is able to help us with describing the kaleidoscope of species on this planet in record time. In recent years, the information content from genome sequencing has rapidly increased and cost decreased, largely due to high profile public and private investments into endeavours like the human genome project. Think about the technological improvements we have seen in computing power – compare the Commodore 64 to your 4gen mobile – well genomics capacity has increased at a rate 50 times greater than that.

It is now possible to derive billions of genetic reads in a matter of hours and to extract DNA from almost any living thing, and a few that aren’t. One of the most exciting developments in biodiversity genomics is DNA barcoding, the sequencing of a standard gene (or genes) to provide a surefire molecular identification. Hundreds of scientists around the world are rushing to DNA barcode their favourite organisms and contributing data to an open-access library – the Barcode of Life Database. The aim is to DNA barcode half a million species in five years – twenty times faster than the rate of traditional taxonomy.

We can apply this DNA barcode library to all sorts of biodiversity management issues – such as discovering our pristine wilderness, identifying global conservation hotspots, and controlling the trade in illegally harvested products such as fish and timber. Perhaps there is new hope at hand for biodiversity in the anthropocene!

Despite our penchant for technology, we remain intrinsically linked to nature. All cultures name species, particularly those that are useful to them. In China a quarter of the continent’s 25,000 plant species are used for medicine and food. However, biodiversity has been undervalued in our Twenty First century economics-driven world.

We care for our pets at home and we feel for the plight of the pandas and orangutans, but we don’t care for the millions of other unknown plants and animals. Yet we must care, since ecosystems of these anonymous species are vital to our survival. They bring us new foods, clean air, clean water, carbon storage, pollination of crops and medicines. It would cost trillions of dollars to attempt to replicate these functions with machines, yet we still do not value the biota that create such essential life supporting ecosystem services.

Industrialisation and technology have divorced our culture from its relationship with nature. We have become a nation of urbanites unable to name even the plants we eat unless vacuum packed and labelled. The loss of connection with nature removes our capacity to care. Perhaps this is where genomics can help. By increasing our ability to know our planet’s biodiversity it can also increase our capacity to care for it. For as Aldous Huxley said “We can only love what we know”. We need to value our earth’s biodiversity, in all its complexity and for its benefits, but first perhaps we need to know it a bit better.

A recording of this lecture can be followed at Life Strikes Back video

This article is covered in an abridged form in InDaily, 15th May 2012. InDaily article – Life Strikes Back

[Featured image: The first whole genome to be sequenced was of the bacterium Haemophilus influenzae. Haemophilus influenzae bacteria cultured on a blood agar plate. Obtained from the CDC Public Health Image Library. Image credit: CDC/Dr. W.A. Clark (PHIL #1617), 1977. Public domain]

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