Category Archives: Life

What should the science fiction of tomorrow look like?

I’ve been reading with interest about Hieroglyph, the first anthology of science fiction stories from Project Hieroglyph based at ASU. The idea is that inspirational science-fiction can aid science:

The name of Project Hieroglyph comes from the notion that certain iconic inventions in science fiction stories serve as modern “hieroglyphs” – Arthur Clarke’s communications satellite, Robert Heinlein’s rocket ship that lands on its fins, Issac Asimov’s robot, and so on. Jim Karkanias of Microsoft Research described hieroglyphs as simple, recognizable symbols on whose significance everyone agrees.

Project Hieroglyph

It’s a description of hieroglyphs that will cause a few Egyptologists to choke, but the idea behind it is definitely interesting. If science fiction inspires future scientists, what modern icons could point in a direction toward the future in science fiction?

In Hieroglyph most of the alternative futures seem grounded in physics, computing or engineering making the collection seem more retro-futuristic. Perhaps the problem of coming up with a 21st century equivalent of a ‘moon-shot’ is that the target is couched in 20th century terms.

Another problem might be the fact be that the Hieroglyph approach might be in reverse to good story-telling. Robert McGrath calls some of the stories preachy, which would suggest that the fiction is there to push the idea. First of all fiction has to work as fiction before it does anything else.

Brian Stableford has argued that good science fiction explores what he calls a novum, a new thing like an invention or discovery. It’s not simply how its use changes the world but also how its unintended use can change human action. He’s pointed out that Asimov’s simple Laws of Robotics remain a fertile source for stories. Bob Shaw was able to pull plenty of ideas from slow glass, which is glass that slows down light so it takes years to pass through it.

Is there is simple iconic biological idea that could inspire science, but is also interesting enough in itself to produce stories?

CRISPR will be a major phenomenon over the next few decades, but by itself it’s not easy to explain, though Carl Zimmer gives it a good effort. Instead, thinking of a use, could pharming become one of Stephenson’s hieroglyphs?

Pulp sci-fi cover

Created with the Pulp-O-Mizer.

Pharming, creating pharmaceuticals with plants, could become a major source of medicines over the next century, along with engineered microbes. The idea itself is simple enough to understand but there are plenty of consequences to explore.

One example is where do you grow the pharm crops? We already know there will be pressure on agricultural land, so will new crops be engineered to grow on marginal land or will the conditions they treat, for people in rich nations, mean they get prime land and drive up the cost of food elsewhere?

Another consequence: Imagine you could engineer a brassica with a variety of benefits to make it a superfood. Like a lot of people, I loathe cabbage and turnip. To nudge people into eating this healthy food, the makers add a mild non-addictive additive to give people a sense of well-being after they eat it. What effect on society could a food like Lotus have? What effect would depriving a society of it have, like if you introduced a pest into a rival country?

I notice that even trying to produce a positive innovation there’s still room for a negative aspect, but even in golden age sci-fi there were dark sides to progress.

I’m sure that pharming isn’t the only possible hieroglyph that botany could offer. I’m sure that there’ something could be done with phytomining, though I’m not sure what and plenty of other things that I’ve missed. Can anyone else think of positive botanical hooks for science fiction and traditional physical sciences based authors overlook?

If you put someone in a room with enough bananas, will they age?

I was driving to a wedding on Saturday, when bananas came up as a topic on the Rhod Gilbert show. The question came up, would putting a banana in bag with an avocado help it ripen? It’s frustrating because it’s one of the few questions he asks that I know the answer to. Listeners were able to help with Huw in Bridgend supplying the information that bananas give off ethene or ethylene, and this causes the avocado to ripen.

Rhod then went on to ask if a banana can accelerate the life of an avocado, could it do that to anything? If you had twins and you put one in a room full of bananas, would she age faster than the twin outside the room? No, but the reason why not is interesting.

If you think bananas make other things ripen by a simple chemical reaction, then it’s reasonable to ask what the effect of filling a room with bananas is. What is surprising about ethylene is how little you need to ripen a fruit. Fruit can ripen when there is a concentration under one part in ten million.

That’s a freakishly low concentration, but it’s not ethylene that directly attacks the fruit. It’s a plant hormone, so it’s something cells use to signal to how they should grow or die. Cells all over a plant can produce it as a means of telling the other cells what’s going on. It’s still odd that a banana ripening could affect an avocado, but ethylene is a very simple chemical and it is used a lot by all kinds of plants.

The fact that ethylene from one plant can affect another means that detecting it is important, but with concentrations being so low, it’s also a challenge. A review in Annals of Botany in 2013 found there was no perfect solution.

Toward the end of the programme another listener sent a message that ethylene can also affect flowers, and the presenters were sceptical. In fact it’s surprising what ethylene is used for by plants. For example, when a shoot is blocked from growing, ethylene can inhibit the elongation of cells, instead causing them to grow wider and stems to thicken to give more push against an obstruction.

It plays a role in leaf abscission, effectively controlling the timing of when leaves fall off. It also effects germination and root formation, among other things. Given the sheer number of things ethylene can do, in some ways it’s a bit of a surprise bananas don’t age people. At least they don’t with ethylene.

There is another feature of bananas. They’re radioactive. Quite a lot of fruit and vegetables are because they have potassium, some of which is naturally radioactive, but bananas come to mind because of the Banana Equivalent Dose.

Radiation doses by Randall Munroe.

Radiation doses by Randall Munroe.

The Banana Equivalent Dose is a way of thinking about the effects of low-level radiation. Eating a banana gives you a dose of 0.1 μSv. In reality it doesn’t work to take this too seriously because the effects of long-term exposure are different to acute exposure. A dose of 4 Sv is usually fatal so if someone were to put (4 000 000 / 0.1 =) 40 million bananas into you instantly then you have a would be a fatal dose, though it’s likely you’d have died from other problems before that.

Using Plant and Crop Extracts to Enhance Rural Household Food Security

Various plants, crops and extracts have been used over several generations to contribute to household food and nutrition security in semi-arid areas (Khan, et al. 2013; , Smith, et al. 2007; Schipper, 2000; Heslop-Harrison and Schwarzacher, 2007; Combrinck, et al. 2007; Flavier et al. 1995). A wide variety of plants are used within a broader knowledge framework termed ‘indigenous knowledge’ (Warren, 1991). However, there is no clear agreement about what exactly constitutes the knowledge paradigm. Despite the lack of clarity, communities use various facets of this concept to tackle complex challenges related to food, education, health care and natural resource management (van Rensburg, et al. 2007). Unfortunately, it is usually not taken seriously as a viable alternative for ensuring food security and nutrition. Many people rely on methods based on the scientific approach and thus IKS may be at the verge of extinction. This, however, is not to imply that the two knowledge systems are mutually exclusive.

General utilization of vegetables in Africa is low and in 1995 per capita consumption of vegetables was 29kg whereas the world average was 75kg/year/person (Maundu 2006). Systematic exclusion of traditional vegetable crops in diets is attributed to many factors including the green revolution, urbanization and changing lifestyles and gross under-valuation of indigenous knowledge systems (Flavier, et al. 1995, Warren, 1991, Kolawole, 2001, Maikhuri, et al. 1999). Consequently, little concerted efforts are being implemented to conserve local gene banks of traditional vegetable seed in Africa. However, in recent years, there has been recognition that traditional vegetables or more broadly orphan crops are highly adaptable to local conditions and therefore important in the attainment of household food security (Pretty and Bharucha, 2014).

Rwanda is a small emerging economy located in East Africa with an estimated population of 13 million (National Institute of Statistics of Rwanda National Demographic Survey, 2012). The country has been experiencing economic growth largely driven by improved agricultural productivity from the government’s Crop Intensification Program and Land Use Consolidation. These programs focus on conventional crops such as maize, Irish potatoes, beans and banana. However, less emphasis is placed on traditional vegetables (TV). This study involved the identification of traditional vegetables found in Musanze District in the Northern Province, their subsequent contribution in the livelihoods of rural farmers in the District and institutional and policy constraints in production. This study also influenced a discussion on FAO FSN forum which explored how different methods of indigenous food preparation are influenced by the changing social, economic, cultural and institutional conditions and how these ultimately determine food security.

Traditional vegetables found in Musanze District, Northern Rwanda

Traditional vegetables found in Musanze District, Northern Rwanda


We conducted a survey in Musanze District specifically in Busogo, Kimonyi and Muko sectors. The sectors were selected randomly from a list of sectors found in the district. The population stood at 314,242 inhabitants on an area of 530.4 km2 implying subsequent density of 592.6 habitants per km2 (DDP Musanze, 2013-2018). The district has a surface area of 530.4 km2 including 60 km2 of Volcanic National Park and 28 km2 Ruhondo lake. It is bordered by Uganda and D.R.C in the North, by Gakenke District in the South, Burera District in the East and Nyabihu District in the West. Currently, Musanze District comprises 15 administrative sectors, 68 cells and 432 villages commonly named Imidugudu.

Multi-stage sampling was used to select 100 farming households in Musanze district. A structured questionnaire administered at the household level was used to collect relevant data for this research. The questionnaire consisted of 5 sections focusing on the identification of the farmer, household economic activities, and utilization of traditional vegetables, agronomic practices used to grow traditional vegetables, marketing aspects and constraints faced during consumption and selling traditional vegetables. Two main tools used for analysis were gross margin analysis and the binary logistic regression model.


Utilization of traditional vegetables

The researchers were interested in ascertaining the quantities consumed of the different classes of traditional vegetables. Most of the respondents consumed Amaranthus, followed by Nightshade (45%), Eggplant (14%), Spider plant (12%), Cucumber 5%, and Nakati (2%). Quantity consumed per week ranged from 0.004 kg to 1.86 kg per household (green weight). Kitchen gardens were used to grow these vegetables and typically between 2-6m2 indicating the land constraint that farmers are facing in agricultural production. Only 5% sampled farmers had access to extension services for growing traditional vegetables. In addition, access to certified seed was a critical constraint.

Kitchen garden in Musanze District

Kitchen garden in Musanze District

Economic profitability of traditional vegetables

We considered both quantities meant for household consumption and also for sale. In cases, where markets were missing, shadow pricing was used to impute economic values to both inputs and outputs. The mean gross income equal to 64 661.88 Frw/month/m2 (US$107), while the total cost was 40368.00Frs/month/m2 (US$68), resulting in a net income of 24293.88Frw/month/m2 (US$40). Traditional vegetables can therefore be considered as an alternative for generating income for the poor in rural areas.

Promoting use among rural farmers

Number of cattle owned, availability of extension support, farm size had a positive and significant effect on the probability of adopting TVs among farmers. Age, household size, education, availability of seeds were not statistically significant (p<0.05). The coefficient of extension support shows that farmers who have access to training have a higher chance of adopting TVs than the untrained farmers. This may be due to the ability of trained farmers to obtain process and use information available on the relative advantages of TVs. Further, training also has the tendency of confidence generation among the farmers resulting in higher rates of adoption. The number of cattle owned positively influenced the probability of TV integration by the household due to the availability of manure. In Rwanda, the government is emphasizing cattle ownership through the One-cow per household initiative.


TVs play an important role in household food security and income generation. However, priority could be put on production, use, consumption, conservation and commercialization programs of Amaranth, Nightshade, Spiderplant , Pumpkin, Nakati, and Eggplant because these are the main traditional vegetables. There is need to enhance awareness of farmers by providing with appropriate extension services. The current National Agriculture Policy does not make explicit reference to traditional vegetables. Instead it emphasizes on staple foods like Beans, Irish potatoes, Rice, Maize, Wheat, Soya bean and Banana. Furthermore, the main programs are:

  • Coffee programme
  • Tea programme
  • Pyrethrum programme
  • Roses programme
  • Exotic fruits programme
  • Ornamental plants programme
  • Beans programme
  • Rice programme
  • Maize programme
  • Wheat programme
  • Soya programme
  • Irish potatoes programme
  • Hides and skins programme
  • Honey programme
  • Meat programme
  • Milk programme

No specific program on traditional vegetables is highlighted. Findings of this analysis have also been confirmed in other countries within the East African Community, and therefore reinforce the idea that TVs could be considered at the national policy level because of potential roles in reducing malnutrition that remains endemic to the region.


Combrinck S., Du Plooy G.W., R. I. McCrindle R.I. & Botha B.M. (2007). Morphology and Histochemistry of the Glandular Trichomes of Lippia scaberrima (Verbenaceae), Annals of Botany, 99 (6) 1111-1119. DOI:

Flavier J.M., De Jesus A. & Navarro C.S. (1995). 43. The Regional Program for the Promotion of Indigenous Knowledge in Asia (REPPIKA), The Cultural Dimension of Development, 479-487. DOI:

Heslop-Harrison J.S. & Schwarzacher T. (2007). Domestication, Genomics and the Future for Banana, Annals of Botany, 100 (5) 1073-1084. DOI:

Kolawole O.D. (2001). Local Knowledge Utilization and Sustainable Rural Development in the 21st Century, Indigenous Knowledge Development Monitor, 9 (3) 13-15. Available via ResearchGate

Maikhuri, R.K., Rao, K.S., Saxena. K.G., & Semwal, R.I., (1999). Traditional Crops In The Central Himalayas. Plant Genetic Resources Newsletter 1999, 120, pp. 1-7 via Negi (2007).

Maundu, P. (2006). Promotion of Under-Utilized Food Plants in Sub-Saharan Africa: Experiences with African Leafy Vegetables, International Plant Genetic Resources Institute via

Musanze District Development Plan (2013-2018). District Development Plan. Available at

Negi C.S. (2007). Changing face of polyculture in the Darma and Johaar valleys, Pithoragarh, Kumaun Himalayas, International Journal of Sustainable Development , 14 (4) 428-436. DOI:

NISR Demographic and Health Survey. 2012. Indicator Reports. 2012. Kigali, Rwanda.

Pretty J. & Bharucha Z.P. (2014). Sustainable intensification in agricultural systems, Annals of Botany, 114 (8) 1571-1596. DOI:

Schippers, R.R. (2000). African Indigenous Vegetables. An Overview of the Cultivated Species. Chatham. UK: Natural Resources Institute/ ACP-EU Technical Centre for Agricultural and Rural Cooperation. Info at

Smith, F. I., & Eyzaguirre, P. (2007). African leafy vegetables: their role in the world health organization’s global fruit and vegetables initiative. African Journal of Food, Agriculture, Nutrition and Development. Online at

van Rensburg W.J., Van Averbeke W., Slabbert R., Faber M., Van Jaarsveld P., Van Heerden I., Wenhold F. & Oelofse A. (2009). African leafy vegetables in South Africa, Water SA, 33 (3) DOI:

Warren, D. M., 1991. Using Indigenous Knowledge in Agricultural Development. World Bank Discussion Paper No.127, Washington, D.C: The World Bank

Effect of light on anatomical and biochemical aspects of hybrid larch embryos

Larch embryos In conifers, mature somatic embryos and zygotic embryos appear to resemble one another physiologically and morphologically. However, phenotypes of cloned conifer embryos can be strongly influenced by a number of in vitro factors and in some instances clonal variation can exceed that found in nature. A recent study in Annals of Botany examines whether zygotic embryos that develop within light-opaque cones differ from somatic embryos developing in dark/light conditions in vitro. Embryogenesis in larch is well understood both in situ and in vitro and thus provides a suitable system for addressing this question.

In larch embryos, light has a negative effect on protein accumulation, but a positive effect on phenol accumulation. Light did not affect morphogenesis, e.g. cotyledon number. Somatic embryos produced different amounts of phenolics, such as quercetrin, depending on light conditions. The greatest difference was seen in the embryonal root cap in all embryo types and conditions.

Effect of light conditions on anatomical and biochemical aspects of somatic and zygotic embryos of hybrid larch (Larix × marschlinsii). Annals of Botany January 20 2015 doi: 10.1093/aob/mcu254

Diversity, distribution and roles of osmoprotective compounds accumulated in halophytes under abiotic stress

Annals of Botany Osmolytes are low-molecular-weight organic solutes, a broad group that encompasses a variety of compounds such as amino acids, tertiary sulphonium and quaternary ammonium compounds, sugars and polyhydric alcohols. Osmolytes are accumulated in the cytoplasm of halophytic species in order to balance the osmotic potential of the Na+ and Cl− accumulated in the vacuole. The advantages of the accumulation of osmolytes are that they keep the main physiological functions of the cell active, the induction of their biosynthesis is controlled by environmental cues, and they can be synthesized at all developmental stages. In addition to their role in osmoregulation, osmolytes have crucial functions in protecting subcellular structures and in scavenging reactive oxygen species.

This review discusses the diversity of osmolytes among halophytes and their distribution within taxonomic groups, the intrinsic and extrinsic factors that influence their accumulation, and their role in osmoregulation and osmoprotection. Increasing the osmolyte content in plants is an interesting strategy to improve the growth and yield of crops upon exposure to salinity. Examples of transgenic plants as well as exogenous applications of some osmolytes are also discussed. Finally, the potential use of osmolytes in protein stabilization and solvation in biotechnology, including the pharmaceutical industry and medicine, are considered.

Slama, I., Abdelly, C., Bouchereau, A., Flowers, T., & Savouré, A. Diversity, distribution and roles of osmoprotective compounds accumulated in halophytes under abiotic stress. (2015) Annals of Botany, January 5, 2015 doi: 10.1093/aob/mcu239

Evolution shaped the internal beauty of plants

Santa Cells

Image by Oliver Leroux.

As plants embraced the terrestrial lifestyle, they underwent a range of adaptations to increase their size and stature as well as to facilitate transport of water and/or solutes. These vegetative innovations, which include the development of vascular and mechanical tissues, increased the anatomical complexity of plants. Such specialization is reflected in the design of the cell walls which surround plant cells in each tissue and fulfill a wide range of roles that are fundamental to plant life. A recently published Special Issue of Annals of Botany features papers focusing on a diverse range of topics pertaining to cell wall diversity and evolution, as well as to cell wall biosynthesis and remodelling.

Plant microscopists take advantage of cell wall diversity and through combination of dyes with affinities for specific cell wall architectures and specialized optics one can display the beauty of the internal structure of plants. The Christmas-inspired image is composed of transverse sections of Equisetum arvense stem (eyes), Acorus calamus root (nose) and Apium graveolens petiole (mouth).

Editor’s Note: You can read Oliver Leroux’s review article Collenchyma: a versatile mechanical tissue with dynamic cell walls for free at Annals of Botany.

The Guardian tackles the ethics of rewilding

The Guardian posted an interesting article yesterday from Tori Herridge: Mammoths are a huge part of my life. But cloning them is wrong.


Mammoth of BC by Tyler Ingram / Flickr.

I’ll concede that a mammoth is not a plant, but part of what I found interesting is that Herridge points out that mammoths didn’t exist in isolation. She tackles the idea that mammoths could somehow be part of a plan to restore the arctic steppes, but she makes an important point:

There’s a reason the terms “de-extinction” and “rewilding” are so powerful and that’s because they imply a return to a time, a state of grace, a place that was somehow unspoiled. Cloning a mammoth offers us the hope of undoing the excesses of humanity, bringing back the creatures whose extinction we helped bring about.

I think the idea of turning back the clock, to a time when things are better, is a powerful image. However it isn’t practical. Herridge points out that the mammoth was part of a wider ecosystem of arctic steppe, and it’s not certain that the plants will naturally appear if you dump a load of mammoths in Siberia.

It’s not even purely about the plants. Looking this up I saw there was a lot about remediation in the Root Biology special issue of Annals of Botany (now free access). In particular, Interactions between exotic invasive plants and soil microbes in the rhizosphere suggest that ‘everything is not everywhere’ say Rout and Callaway. They’re talking about microbes in the context of invasive species, but I wonder what ten thousand years of change has done to the soil of the arctic.

We don’t have the plants, we may not have the right soils. We are going through a big extinction event. I’d love to see a mammoth, but sadly when you look at the social problems a mammoth would have, as well as the many conservation efforts competing for limited funding, I think Tori Herridge is right, and that she does a good job of explaining all the problems.

Is there a downside for plants when they can’t sense ‘up’?

Looking at a tree, it can be hard to visualise the sheer volume of water being drawn up from the roots to the canopy. That volume of was is massive, and puts cells under a lot of pressure, so lignin, the substance plants use to strengthen cell walls, is an important product. But what happens to lignin if you take gravity away? Growth and Lignification in Seedlings Exposed to Eight Days of Microgravity by Cowles et al. is a study that aims to find out.

The experiment on STS-3 was growing pine seedlings with mung beans and oat seeds. There were a couple of targets. One was to examine how gravity affected the production of lignin. The other was to test the PGU, the plant growth unit, that would be used in following missions.

Plant Growth Unit

From Cowles et al.

To see the effect of gravity a PGU with similar plants was kept on Earth, so the development of the plants could be compared.

Germination of the orbiting plants was much like the 1g plants. However, Cowles et al. point out that the seeds have to be prepared before launch, which gave them twelve hours on Earth to germinate. They found that the flying plants grew less, and in the case of the seeds, roots were growing ‘up’ as well as ‘down’. Some of the plants that grew in orbit also contained less lignin.

There have been plenty of papers that went on to cite this research, most recently Expression of stress-related genes in zebrawood (Astronium fraxinifolium, Anacardiaceae) seedlings following germination in microgravity by Inglis et al. in Genetics and Molecular Biology from this year.

Recently in Annals of Botany there’s been Xylem Development and Cell Wall Changes of Soybean Seedlings Grown in Space and in the opposite directon Hypergravity Stimulus Enhances Primary Xylem Development and Decreases Mechanical Properties of Secondary Cell Walls in Inflorescence Stems of Arabidopsis thaliana by Nakabayashi et al.

This is interesting that it still gets cited because the results weren’t all significant. While the mung beans had less lignin, the oat and pine seedlings didn’t have significantly less and the experiment was relatively small. However, this flight wasn’t just about the results, it also worked to establish a method. By laying out the experimental technique used to analyse the plant Cowles et al laid down a baseline for other researchers to compare and improve their techniques.

The basic question they studied remains important. Understanding the processes that produce lignin could help with technology on Earth. For example, it would be helpful in producing biofuel if there were less lignin in it to start with. Launching plants and growing them in space would be a spectacularly inefficient way to do that. However for small samples, it can be a useful way to isolate one variable and help figure out the mechanics of lignin production.

You can read more posts on papers from our spaceflight supplement by clicking the STS-3 tag.

Today’s Papers

Cowles J.R., Scheld H.W., Lemay R. & Peterson C. (1984). Growth and Lignification in Seedlings Exposed to Eight Days of Microgravity , Annals of Botany, 54 (supp3) 33-48. DOI:

Chapple C. & Rick Meilan (2007). Loosening lignin’s grip on biofuel production, Nature Biotechnology, 25 (7) 746-748. DOI:

de Micco V., J.-P. Joseleau & K. Ruel (2008). Xylem Development and Cell Wall Changes of Soybean Seedlings Grown in Space, Annals of Botany, 101 (5) 661-669. DOI:

Inglis P.W., Ciampi A.Y., Salomão A.N., Costa T.D.S.A. & Azevedo V.C.R. (2013). Expression of stress-related genes in zebrawood (Astronium fraxinifolium, Anacardiaceae) seedlings following germination in microgravity., Genetics and molecular biology, PMID:

NAKABAYASHI I. (2006). Hypergravity Stimulus Enhances Primary Xylem Development and Decreases Mechanical Properties of Secondary Cell Walls in Inflorescence Stems of Arabidopsis thaliana, Annals of Botany, 97 (6) 1083-1090. DOI: