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Genetic modification could bring us closer to fuel security

By Rebecca Nesbit

Happy New Year! Last year I blogged about the challenges and promises of second-generation biofuels (those made from agricultural by-products such as straw or from woody plants such as poplar). If these crops are going to be a relatively cheap and sustainable alternative to fossil fuels, we will have to think seriously about genetic modification.

Rice is one of the most important food resources in the world. Its cultivation means about 800 million metric tons of rice straw is also produced annually, which is normally burned or decayed in the field. Getting rid of the straw in this way produces greenhouse gasses such as methane. But what if we could use straw, currently a polluting by-product, as a source of energy?


Woody plants, including the inedible part of food crops, get their strength from lignin and cellulose. Cellulose is basically lots of glucose molecules joined together, so a perfect energy source. But the problem is how to turn it into ethanol to use as biofuel.

The process currently relies on enzymes from bacteria or fungi, but it is extremely expensive. If these enzymes could be produced by GM plants rather than by micro-organisms, the production of ethanol would be cheaper and quicker.

Scientists from Taiwan genetically modified rice plants to contain a gene from a bacteria which produces an enzyme that breaks down cellulose. The enzyme they chose has the advantage that it works best at high temperatures, and doesn’t work well to break down cellulose in conditions found in the field.

They managed to produce rice straw with high levels of the enzyme in it, so with potential to increase the efficiency of biofuel production. The enzyme remains stable in the straw long after the rice has been harvested, and becomes active at higher temperatures.

By choosing an enzyme that only breaks down cellulose at high temperatures, this shouldn’t stop the plant growing normally. However, they found some evidence that the genetically modified plants were shorter, so more experiments are needed to work out whether adding the gene for the enzyme disrupts the growth of the rice.

There are clear environmental benefits to using agricultural waste as a replacement for fossil fuels and to making the process of biofuel production more efficient. But is genetic modification a viable, sensible, or even essential option? As always, I’ll be interested to hear your views.
Chou, H., Dai, Z., Hsieh, C., & Ku, M. (2011). High level expression of Acidothermus cellulolyticus beta-1, 4-endoglucanase in transgenic rice enhances the hydrolysis of its straw by cultured cow gastric fluid Biotechnology for Biofuels, 4 (1) DOI: 10.1186/1754-6834-4-58

Campaign: Biofuel subsidies could damage wildlife

The Government is proposing to susidise bioenergy projects as it tries to meet renewable energy targets. Its plans, according to the RSPB, are potentially damaging to habitats and do not deliver necessary reductions in greenhouse gas emissions.

By 12th Jauary, the RSPB are asking people to send a letter or email urging the Government to stop subsidies to large-scale energy-only plants. The details of what the problem is, what to say, and where to post it to can be found here. This campaign is by no means anti-biofuel, it is just anti the proposals as they stand.

I’ve just written – it shouldn’t take long!

Biodiversity offsets – an efficient way of protecting seabirds?

by Rebecca Nesbit 

Each year, 7.2 million tonnes of fisheries catch gets thrown away as bycatch, including fish, turtles and birds.

Modifying fishing gear is a popular way of reducing this, and to a large extent it can often be effective. However, suitable modifications aren’t always possible, so preventing fishing in certain areas can be the only way to solve the problem. As I’ve blogged before, this brings its own challenges.

A recent paper in PLoS looked at options of biodiversity ‘off-setting’ for seabirds caught as bycatch, much in the same way that carbon offsetting is popular for plane travel. It’s widely acknowledged that this isn’t a long-term solution, but in the short term it may be possible to save more birds by putting money into conservation schemes than it would be by modifying equipment or creating exclusion zones.

Tuna and squid fishing in particular leads to a bycatch of albatross, petrels, and shearwaters which get caught on the hooks of longlines. However, these birds often face a far greater danger in their breeding grounds from invasive mammals, particularly rats and feral cats, which have decimated many seabird colonies. The problem is so severe that most vertebrate extinctions over the past six centuries have been caused by invasive mammals.

To test the idea of biodiversity offsets, this paper uses the example of the tuna fishery which stretches along the east coast of Australia. The main victims here are flesh-footed shearwaters. Possible solutions include only laying lines at night and weighting the lines so they sink out of reach more quickly. These have helped but they can’t eliminate bycatch, and they’re expensive, potentially dangerous to use, and hard to enforce. The authors point out that “like world peace, bycatch elimination cannot be achieved over night”.

The shearwaters are also facing threats in their island breeding colonies, including habitat loss, ingestion of plastic, and predation by rats.

Hopefully, better technical solutions to reducing bycatch will be available in a few years time, so rather than implement what we currently have available, it’s perhaps better to look to other conservation measures to give the shearwater population ‘breathing space’ until a real solution is found. Eradication of rats would benefit the whole island ecosystem, not just the shearwaters. In the example of the flesh-footed shearwaters, eradicating invasive rodents is at least 10 times more cost effective than closing areas of sea to fishing.

The way I see it is that, if I was given a pot of money to save seabirds I would spend it on saving the most birds possible. So if the fishing industry has money to use for conservation maybe it is best put to use on islands not boats. However, biodiversity offsets should be a way of saving more birds, not of saving money.

Another interpretation is, of course, that we shouldn’t eat tuna. It’s delicious, and I do miss it…

Pascoe S, Wilcox C, & Donlan CJ (2011). Biodiversity offsets: a cost-effective interim solution to seabird bycatch in fisheries? PloS one, 6 (10) PMID: 22039422


Why is biodiversity important to you?

by Rebecca Nesbit 

Foreign adventures often get me thinking, and things I’ve learnt can inspire interesting discussions in real life and on our blog. I have just returned from a trip to Gibraltar and southern Spain – great food, friends and birding. Some of these friends are from the Gibraltar Ornithological and Natural History Society, and this post was inspired by our discussions.

We are all intending to dedicate our careers to protecting biodiversity, and at GONHS they are doing some great work. But when we got onto the question of ‘why’ it emerged that my ultimate motivations were different to some of my friends’. ‘It’s intrinsically valuable’ ‘I protect biodiversity for its own sake’ ‘We messed it up, it’s our duty to protect it’ were arguments put forward, but actually rather different to mine yet are equally valid.

I protect biodiversity for people. We benefit in so many ways: directly from enjoyment (and this isn’t to be underestimated – being around nature has major health benefits), and indirectly from services such as pollination and water purification.

I’m also interested in the wellbeing of other animals who have some kind of ability to feel ‘happiness’. The line is fuzzy and we will never understand exactly what this means, but the point is that my views are about happiness and not necessarily about humans.

I am intrigued to hear the views of more people so I have devised some questions, and hope the discussion will continue in comments at the bottom. If you have received this by email you need to go to the blog to tick your answers to my questions: http://thesciencesays.southernfriedscience.com/biodiversity-questions

It’s also a good chance to share some photos – hover the mouse over these to name the species.

Why is biodiversity worth protecting?

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Rebecca Nesbit's environment blog: what is the importance of biodiversity?

If you could release a single species that would wipe out many others so reduce biodiversity, but would increase human happiness, would you do it? (assuming no animals suffer)

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Rebecca Nesbit's blog: why is biodiversity important?

If humans and animals were about to go extinct would you work to ensure the diversity of plants remained once we are gone?

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Is it important to protect a great work of art even if no human would ever see it again?

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Rebecca Nesbit's blog: why is biodiversity important?

Exotic trees don’t taste so good

by Rebecca Nesbit

In many parts of the world, pastoralists lose the grazing they rely upon when they are evicted by forestry agencies, often planting exotic trees. Herders rely on fodder trees in particular because their deep root systems ensure they provide feed even in the dry season. This means that even herders who are allowed to remain on the land have had an important resource replaced with non-native species.

In Northern Pakistan large slopes were planted with exotic trees to overcome deforestation and land degradation caused by over grazing. However, the species weren’t chosen to meet the needs of herders, who lost a resource they relied upon.

As a result, the average herd size owned by each landless pastoralist decreased from 340 to 140 goats and sheep. A quarter of herders gave up their flocks altogether and looked for work. Anyone who owned land on the hillside, however, benefitted because they could sell wood as fuel.

Although the trees are planted to stabilise the overgrazed hillside, they inadvertently cause overgrazing elsewhere. The exotic trees are no good as fodder, and this forces herders to spend more time at both upland and lowland grazing areas, which leads to overgrazing there.

A 2011 paper published by scientists from Switzerland and the University of Central Asia looked at alternatives. They showed that indigenous tree and shrub species have great potential to sustain the pastoral system. The authors identify a range of native species that will provide fodder and shade at different altitudes. These would be viable alternatives to the exotic tree plantations of current afforestation programmes.

As well as damaging the livelihoods of pastoralists and leading to overgrazing elsewhere, planting of exotic trees has led to social tensions as different groups compete for resources. By providing an essential resource, native fodder trees should help stabilise social relationships among landowners, sedentary farming tenants, and landless herders. Promoting these trees can also enhance food security for communities in the mountain valleys of Northern Pakistan.

Shrinking grazing areas are detrimental to the mountain environment and to the livelihoods of local communities. This paper gives hope for improved management techniques which could reduce the effect of shrinking grazing. Happy herders, happy sheep.

Inam-ur-Rahim, Daniel Maselli, Henri Rueff and Urs Wiesmann (2011) Indigenous fodder trees can increase grazing accessibility for landless and mobile pastoralists in northern Pakistan Pastoralism: Research, Policy and Practice, doi:10.1186/2041-7136-1-2

New technologies in bioethanol production

by Rebecca Nesbit

In the race to achieve fuel security and to reduce our reliance on fossil fuels, the US has rapidly increased the volume of bioethanol it produces, from 6.2 billion litres/year in 2000 to 50 billion in 2010. Ethanol has the advantage that it can be mixed with petrol so cars need no conversion. However, most of this growth in ethanol has been from first generation corn ethanol, produced through fermentation. First generation biofuels  have the major drawback that they are energy intensive to produce, which can counteract any reduction in green house gas emissions. Also, there is a raging food vs fuel argument surrounding biofuels made from food crops.

To overcome some of these problems, research is taking place into second generation biofuels, made from materials such as forestry wastes, grasses, wastepaper etc. These can be converted into liquid fuel, normally using enzymes. But pre-treatment steps are needed to make the enzymes more effective, and options include grinding, adding acid, steaming, or treatment with fungi. Many of these, however, haven’t made it out of the lab. A paper available this month from Biotechnology for Biofuels predicted trade-offs between different pre-treatment steps for commercial ethanol production from grass straw.

For the same amount of straw put in, using dilute acid, dilute alkali or hot water as pre-treatments produced similar quantities of ethanol. Steam explosion pre-treatment was slightly less effective so yielded less ethanol.

Costs of the plant were highest for alkali pre-treatment, and similar for the other three options, with steam being the lowest. The ethanol production costs varied by a few cents per litre ($0.84 per litre for dilute acid, $0.89 for dilute alkali, $0.81 for hot water and $0.86 for steam explosion). Water use also varied – the thirstiest treatment actually being alkali not water.

They concluded that ethanol price and energy use were highly dependent on the pre-treatment technology, demonstrating the importance of addressing the tradeoffs in costs and environmental impacts of different aspects of the pre-treatment.

New technologies are set to make bioethanol more efficient and less energy intensive to produce, which in turn reduces its environmental impact. Biofuels made with current technologies may give biofuels a bad name, but as technologies making second generation biofuels viable move beyond the lab, their environmental impact will reduce. And there don’t seem to be many viable options available for feeding our cars, so research such as this can shape our future fuel supply.

Deepak Kumar and Ganti S Murthy (2011) Impact of pretreatment and downstream processing technologies on economics and energy use in cellulosic ethanol production
Biotechnology for Biofuels, 4:27 doi:10.1186/1754-6834-4-27

Dreaming of a world where science is free

by Rebecca Nesbit

I wanted to share some thoughts from the Science Online conference in London, which was eye opening on a far wider range of topics that I had imagined. The internet has changed not just the way we can communicate science but also ways we do science.

Open science is a hot topic at the moment – i.e. making both data and results available to everyone. Open data means that information collected by one group of scientists can be used to its full potential because other scientists can analyse it in new ways. The ideal of open science is to have journal articles freely available too.

There is a move in this direction; journals which don’t charge for articles, such as BioMed and PLoS, have become well respected. But, while we were talking about how publishers are changing their business models to make journals free online, Ben Goldacre was blogging about a fellow at Harvard’s Centre for Ethics who has just been arrested for downloading 4.8 million papers with the intention of making them freely available.

I’m up for anything that will advance our understanding science, and data sharing is definitely in that category. I also believe that making journal articles available is at least as important, not just because I no longer have a university log in to get them free myself (sob). Knowledge shouldn’t be elitist, and to researchers in developing countries free access to journals can be invaluable. So open science is a great aim, but there are barriers.

I admit I’m a capitalist as well as a scientist. Journals need to make their money somehow. In the past they have charged for their articles, but to make articles free they need money from grants or advertising, or from charging authors.

In some cases it wouldn’t be financially viable to collect data if it was going to be freely available. If pharmaceutical developers had to let their competitors access their data it wouldn’t be worth their while collecting it – so that’s a situation where open access doesn’t advance our scientific understanding. In fact, it stops science being done.

There are confidentiality barriers too. For example, I read last week about a tobacco company wanting to get its hands on data from surveys about teenagers’ smoking habits. Open access in this situation doesn’t seem to be the ethical choice…

We’re on a long and difficult path to making the most of the opportunities technology offers us. The conference sparked interesting discussions about the cultural changes we need to make open science work. For example, changing the way we judge a scientist’s success. It’s a cut-throat fight for funding at the moment so anyone who wants to stay in the game can only dedicate resources to activities they will be rewarded for.

In case you were wondering what this has to do with birds, bees or feeding the world, it’s because science is fundamental to conservation and food security. If open science helps advance our understanding of science and social science then it helps tackle these issues.

Also, making journals freely available to anyone with the internet doesn’t make the science available. Papers can be time-consuming to read, complicated, and written in inaccessible language. The conference made me realise that open science is what I’m blogging for – to help more research escape from the academic world and into the real world. Thanks for reading it!

More than just calories

by Rebecca Nesbit 

In today’s population of just over 7 billion people, more than 900 million are undernourished and over 2 billion have nutrient deficiencies, yet over 1 billion adults are overweight. Lots of work has gone on to address the problems of undernourishment and obesity, but the problem of nutrient deficiency has taken second place.

Much of the world has moved towards growing fewer types of foods, and in many places agriculture is now dominated by cereals. However, diverse diets generally provide greater nutrition and have been associated with health benefits, from lower mortality rates to a reduced chance of developing cancer.

In sub-Saharan Africa 40% of children are chronically undernourished or stunted, and food security initiatives must take nutrients as well as calories into account. A study recently published in PLos ONE examined diet diversity in villages in Malawi, Rwanda and Kenya where malnutrition and food insecurity are high.

Rebecca Nesbit, Food security in Africa requires the right nutrients as well as enough food
To measure diet diversity, the study successfully used a technique that is usually applied to species diversity. They produced a value for each individual farm, where a higher value means the farm’s produce provides greater nutritional diversity. The value is based on the number of plant species on the farm with unique nutritional make-ups. It’s different to simply recording the number of species because some types of food will have the same nutritional content.

Quantifying things in this way helped them identify which species were particularly important – i.e. those which provided the nutrients that none of the other foods did. Mulberry, for example, provided vitamin B complexes.

It also provided interesting insight into redundancy, which refers to how many species there are with each nutritional composition. Two farms may have the same value for nutritional diversity, but if one has a greater redundancy then it is less vulnerable if individual species are no longer grown, perhaps due to disease or changing climatic conditions.

The study found variation between the farms in the values for nutritional diversity, for example mineral diversity was lower in Malawi than Uganda or Kenya. The soils in these Malawian villages were also poorest. This could mean villages are unable to grow such a range of plants, or the low fertility could be precisely because they only grow a small number of species.

Decades of research have given us a better understanding of how the body uses nutrients, allowing us to consider all these nutrients together when planning agricultural systems to increase food security. This paper explains the importance of nutritional diversity and comes up with a practical way of measuring it.


Remans R, Flynn DF, DeClerck F, Diru W, Fanzo J, Gaynor K, Lambrecht I, Mudiope J, Mutuo PK, Nkhoma P, Siriri D, Sullivan C, & Palm CA (2011). Assessing nutritional diversity of cropping systems in African villages. PloS one, 6 (6) PMID: 21698127

Conservation and industry side by side

by Rebecca Nesbit

The relationship between conservation and economics is a complex one. We rely on the natural world for vital services. Without these we wouldn’t even have an economy – they are everything from pollination through to water purification and climate regulation. But on a local scale there are often trade-offs, at least in the short term. Saving endangered species can be expensive.

A paper published this month by researchers from the University of Alberta (Canada) looked at a trade-off between proposed industrial developments and protecting habitats the industry would destroy.

How you choose which areas of land to preserve is a much-debated issue. In this paper they worked on the premise that by protecting every ecosystem type in the area most species will have their needs met.

Oil and gas extraction and forestry occur across much of Alberta’s forested areas. There is concern that the cumulative environmental impact of this isn’t being addressed, particularly in the oil sands. As a result there are plans to create biological reserves to protect the species within them. This paper takes a new approach to choosing where to locate these reserves, based partly on the trade-offs between conservation targets and economic costs (including lost revenue from not using that land for industry).

They found that the proportion of the area which is protected could double from 15% to 30% while maintaining access to 97% of the region’s resources. This is partly because the presence of oil sands means much of the valuable resources are concentrated in a small area. So the oil sands can be seen as an enabling factor for conservation in Alberta, not a barrier; economic activity can be concentrated in a small area yet provide valuable revenue which can be directed towards conservation nearby. Of course other environmental concerns about the industry, such as pollution, still need to be addressed.

Choosing reserves based only on the economic value of the resources within them, however, doesn’t maximise their biological benefit. When coming up with the best reserve design for the region the study also took into account how connected the reserves were. Small isolated reserves are often less successful because populations within them often go extinct and are not replaced through migration. The study instead suggested three new large reserves.

It’s good to see a move away from pitting industry and conservation against each other, but recognising that they are essentials which must occur alongside each other. The authors of the study hope their approach will be applied more widely to make wise choices about the design and location of nature protection areas and of industrial developments.

Schneider, R., Hauer, G., Farr, D., Adamowicz, W., & Boutin, S. (2011). Achieving Conservation when Opportunity Costs Are High: Optimizing Reserve Design in Alberta’s Oil Sands Region PLoS ONE, 6 (8) DOI: 10.1371/journal.pone.0023254

Social development means cleaner Chinese cities

by Rebecca Nesbit

As people around the world leave their homes in the countryside to seek a new life in the city there is increasing concern about the impact of urbanisation on the environment. But the effect of urbanisation varies significantly around the world, and there are lessons to be learnt about how the growth of cities can be managed more sustainably.

I readily admit that some cities make me feel the ideal of sustainability is impossibly far off, and days in China without seeing the sky because of the smog are the most depressing. But this is somewhat misguided; China may have a harder task than Europe to make their cities sustainable but it’s on the agenda.

In the 1990s the state government of Jiangsu province set a development goal of ‘a healthy and ecological city’. A growing environmental awareness in China led to an increase in environmental protection infrastructures and to an increased proportion of green space in built-up areas. However, rapid urbanisation since 2000 has led to a huge increase in industrial pollutants being discharged into the environment. Land use changes caused by the growth of urban areas is seen as one of the biggest problems because it causes dramatic changes to biodiversity, local climate and water resources.

New research published in Ecological Indicators made predictions about the effect of urbanisation, and how the environmental impact varied with different models (i.e. whether the process is driven by an influx of people, increased sprawl or rapid economic growth).

They found that social urbanisation, characterised by investment in social development, is likely to have the least impact on the environment. In this scenario the proportion of government expenditure which goes on culture, science, technology, education and health is increased. The study predicted that industrial waste air emission will be lower than in other paths of development and the amount of forest and green space will be higher. It is, however, likely to result in a slower rate of economic growth, but then we have already questioned the wisdom of our obsession with an increasing GDP.

This is further proof that social and environmental issues are interconnected, and offers hope that a sustainable society may not be a richer one but could well be a happier one.

Rebecca Nesbit: sustainability and urbanisation in China, Asia.

Many of my photos of spectacular Chinese city-scapes depict a blanket of smog

Liu et al. (2011) An integrated sustainable development approach to modelling the eco-environmental effects from urbanization. Ecological Indicators 11(6): 1599-1608