Science without the jargon

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Image credit: vividbiology.com (CC BY 4.0)

Have you ever read a scientific paper and struggled to understand the main findings of the research? If so, you are not alone.

When I worked as a research scientist one of my biggest frustrations was how difficult it could be to read research papers, even those within my own field. Research papers are written in a very formal style with lots of jargon, long words and lots of nouns, which help to keep the word count down but also make the text harder to read.

Don’t get me wrong, I’m not “anti-jargon”, I do think that careful use of jargon in articles meant for a specialised audience can be very helpful to readers. For example, using the term “photosynthesis” in a scientific paper on leaves is going to be much more concise and less clumsy than writing “the process by which some organisms use energy from sunlight to convert carbon dioxide and water into sugars” several times.

However, researchers working in different fields can all use different sets of jargon (like different dialects in a language) to the point that a plant scientist like me may not be equipped with the right vocabulary to understand a neuroscience paper (without a significant amount of googling and head-scratching at any rate). New technologies and advances in one field may be relevant to researchers working in other fields, so using different scientific dialects may delay the spread of new knowledge. Another issue is that a lot of scientific research is funded by public money and therefore should be answerable to the public. So how can we make the findings of scientific research more accessible to anyone who is interested?

The media play a big role in communicating the findings of research to the wider public. However, the media can only highlight a tiny fraction of research being published, and they (understandably) focus on the most exciting, weird or funny discoveries. But what about all the other research that might still be of interest to to other scientists and members of the public?

One way that some journals, medical charities and other scientific organisations are making research more accessible to broader audiences is by publishing summaries of research articles written in everyday language using few technical terms. This includes eLife (the journal I work for) and my current job involves producing plain-language summaries called “eLife digests” (you can read a selection of eLife digests on our Roots and Shoots blog.

To highlight the plain-language summaries eLife and other organisations produce, we (the eLife features team) have recently published a collection called “Plain-language summaries of research”. The collection includes articles and blogposts about the experiences of various organisations as well as our advice on how to write plain-language summaries. Furthermore, you can listen to my colleague Stuart King and I discuss plain-language summaries in the latest eLife podcast, episode 37.

The most exciting thing I learned while working on the collection is that there is an enormous variety of plain-language summaries out there covering different areas of science from astrophysics to ecology. Furthermore, different organisations target their summaries at different audiences. For example, the summaries produced by some medical journals and medical charities are often primarily aimed at patients and their families. On the other hand, some journals (e.g. PNAS) produce summaries that are aimed at other scientists who read the journal. I think all of these different approaches have a place in widening access to scientific research.

To help people find plain-language summaries on topics that interest them we have compiled a list of over 50 organisations that produce them. Please do make use of this list, and let eLife know of any other organisations that should be included.

 

A community repository of plant illustrations

Guest post by Erin Sparks, Guillaume Lobet, Larry York and Frédéric Bouché

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It is midnight on a cold winter evening and you are scheduled to give a seminar at 8 am the next morning. All you are missing to complete your presentation is one last graphic to illustrate your conclusions. You wearily open Adobe Illustrator, stare at a blank artboard and think “isn’t there a better way?” What if there was a place where you could access community plant illustrations to use or modify? Good news! A Plant Illustrations Repository is now available to the plant scientific community!

In a time when scientific communication is becoming increasingly important, one method of communication is through illustrations and graphics. For example, graphical abstracts are now frequently employed by journals to summarize the contents of a manuscript and provide a visual overview of the work. These graphics are generated in programs such as Adobe Illustrator, Inkscape, or even PowerPoint. For additional information about graphical abstracts, we refer the reader to this blog post and a recent webinar by Fred entitled: “Communicate your Research Efficiently Using Graphical Abstracts” hosted by Plantae and the American Society of Plant Biologists.

In an effort to promote scientific communication and the use of graphical abstracts, we have initiated a repository for community-generated pictures and vector graphic illustrations of plants. It takes a lot of effort to make vector graphics so we might as well share them among the community. Thus our goal was to provide a central location where plant scientists can contribute their images and graphics to be used or modified by others (and you get credit for it!).

We decided to use a figshare Collection for a couple of reasons:

  • It is free to use and any scientist can deposit data there in a couple of clicks.
  • One dataset can contain more than one file (for instance, .ai + .png + .pdf).
  • It provides unlimited storage for data that are made public.
  • It provides each public dataset with a doi (digital online identifier), which make citation possible, even for a single figure.
  • Finally, the Collection feature of figshare allows us to collect images and illustrations from multiple accounts (yours!) into a single place and to present it nicely!

We invite you to visit the Plant Illustrations Repository to learn more about contributing and utilizing this resource.

Happy Communicating!

Erin, Guillaume, Larry and Fred

 

Erin Sparks is a Postdoc with Philip Benfey at Duke University and her recent work focuses on understanding the development and function of maize brace roots. You can follow Erin on Twitter @ErinSparksPhD

Guillaume Lobet is an Associate Professor at the Forschungszentrum Jülich in Germany and the Université catholique de Louvain in Belgium. His work focuses on the development of whole plant models. You can follow Guillaume on Twitter @guillaumelobet

Larry York is an Assistant Professor at The Samuel Roberts Noble Foundation in Ardmore, OK, USA. His work focuses on root functional phenomics including high-throughput phenotyping of root system architecture and physiology. You can follow Larry on Twitter @LarryMattYork

Frédéric Bouché is a Postdoc with Rick Amasino at the University of Wisconsin-Madison. His work focuses on the identification of the genetic mechanisms controlling the timing of flowering in the model grass Brachypodium, a species closely related to wheat, barley, and oats. You can follow Fred on Twitter @Frederic_Bouche

Note: This post has been published on several sites on the same day to help spread the word about this new community resource.

The rules of spacing

Guest post by Luke Simon

I was at a Christmas party in conversation with a local engineer who, hearing I design food forests, wanted to pick my brain on apple trees. He had six trees in two rows of three, well spaced in his backyard. He was throwing out terms about the mainstream organic sprays he was using, and framed his questions expecting me to know some super organic spray, or spray regimen, that would fix his problems of pests and low vigor in general. I don’t think he expected the answer I gave: ‘What’s planted around the trees?’

We often think of the rules of spacing as rules for keeping other plants away from each other. In practice I find the lines blur between species, and enters a much more broad science: it’s what should be included near the plant, as well as what shouldn’t. Between these two aspects, you make or break the majority of fruit tree problems.

The lines often blur between species because, let’s face it, plants don’t grow in a vacuum and always have something growing up against them. In this guy’s case, his trees were planted right into his lawn. They were in competition with the grass.

Looking at their history, grass and trees are in most cases nemesis of one another. Trees make forest; but grass needs open space. The setting in most yards of trees with grass between is quite artificial, and only exists because we keep the grass mowed. In any other situation, trees would take over.

The prairies are the kingdom of grass, and these occured because of rain shadows, or areas where circumstances such as the Rocky Mountain range messed with the winds that carry rain, creating droughts in one part of the year, and near flooding in another. Trees don’t like that, because most have relatively shallow roots, as much as 80 percent residing in the top three feet of soil depending on the kind and its conditions; but prairie plants, such as the grasses, and Nitrogen fixers like Senna hebecarpa, put roots down unusually deep, so reach the water table whether rain comes or not.

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An experiment showing the root growth of Red Delicious apple tree two years after planting.

Have you ever wondered as you pass woods how the trees survive so close? If you were planting an oak tree in your yard that would someday reach a hundred foot tall, can you imagine the spacing recommendations? They would be over fifty feet apart. Most yards couldn’t fit more than one tree. But in the woods they stand on top of each other, growing for hundreds of years, happy, and healthy.

Studies have shown that trees can grow their roots deep into the ground, but prefer to keep their roots higher in the soil if possible. There is more organic matter, hence nutrients and water, in this layer. If there isn’t, trees will try to put in the work to grow deeper. This is a lot more work, and certainly isn’t their first choice.

What trees really prefer is building networks in which they share and preserve resources. For instance, trees have what is called hydraulic redistibution, which is a fancy term for moving water not only up for their own use, but back down into the soil for storage, and horizontally to other plants. Peter Wholleben, in his book The Hidden Life of Trees recalls his surprise when he found a ring of roots from a beech tree that must have been cut down well over a century beforehand, but still had green, living roots showing above ground. It had no leaves, and the stump was gone. As he explained, citing various studies, the living trees around this ancient (should be dead) tree were feeding it sugars made in their leaves, keeping it alive. Likely, they got some kind of kickback from the extended root system because it allowed them access to more resources.

This is in ancient, established forests, so conditions aren’t quite the same for our young transplants. We can get some similar effects by growing fruit trees in more open settings, or riparian zones. These are zones similar to fencerows and overgrown fields where grasses are just converting to trees. These zones are iconically untidy and wild; but skillful gardeners know the elements of these zones, like clay in a potters hand, have the best potential to form the most beautiful, lush gardens.

Riparian zones have many layers, with notably high numbers of low growing herbaceous and woody shrubs, many of which are nitrogen fixers. The quickest way to simulate this ecology is making ‘guilds’ of plants right around your fruit trees. Here is my manual of bed building for info on quickly clearing grass without tillage. Plan on expanding these plantings every year until the beds around your trees meet. If the tree is older, and larger, the bed should extend at least a couple feet beyond its drip line.

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An example guild. 1. Fruit tree 2. Comfrey 3. Siberian Peashrub 4. Amorpha fruticosa 5. Japanese Wineraspberry 6. Honeyberry 7. Blueberry 8. Turkish Rocket 9. Crambe cordifolia 10. Stepping stones, (or in this case, stepping logs). The green base is a ground cover of mint.

Any guild should include at least 2 woody nitrogen fixing plants, about 5 plants that do not fix nitrogen but can be cut for mulch, such as comfrey, or a groundcover of something like mint, then several fruiting shrubs like raspberry or honeyberry, and some perennial vegetables.

This is the best method if you already have fruit trees in the ground, like our engineer friend. If you’re just planning your food forest, Robert Hart, the father of the northern food forests, recommended planting full size or standard fruit trees at recommended spacing for their size, in rows like any orchard, but then semi standard or medium trees, then dwarf trees, then shrubs, then herbaceous plants, then vines to climb and fill in the cracks between them.

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I’d recommend mulching as much as you can, and planting that area with a complete planting like this. The space should be completly filled with plants, and will establish faster with less work overall.

This system gives quite attractive results that are increasingly less cost and labor than serial applications of even organic, clay-based sprays, pyrethrums and neems, let alone harsher chemicals. There is work later on, but this is of course debatable, because its mostly harvests of fruit. Sounds like pleasant work to me.

This article was originally published on Mortal Tree on 24th February 2017.

About the author: Luke Simon is garden manager for Simon Certified Organic Family Farm, and on his own time a permanent edible landscape designer in Ohio, United States. He is the author of PASSIVE Gardening and Mastering the Growing Edge. Follow him on his blog, Mortal Tree, and his Instagram @mortal_tree.

 

Emerging from the cloud

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Spring lunchtime in Cambridge Botanic Garden

Regular readers of this blog will have noticed that I’ve been rather quiet this year. The main reason for this is that 2016 has not been kind to me. Following the loss of my oldest friend in January, several other things have hit my personal life this year including ill health (both to myself and members of my family) and the loss of my grandmother. These things have left my mental health in a more fragile state than normal so, to look after myself while keeping up with my day job and other responsibilities, the blog has had to take a back seat.

I don’t want to give you the impression that 2016 has been a complete disaster for me. I still enjoy my job at eLife and have taken on some new responsibilities this year, including managing the eLife podcast. In January I set up a new Girl Guide unit, which meets regularly to provide 10-14 year old girls in my local area with opportunities to have fun and learn new skills. We have a lot of fun at our meetings and the numbers of girls in the unit has gradually grown over the year. My friends and I have made good progress with the work on the run-down allotment plot we took on earlier this year. Most importantly, this year has highlighted how wonderful my friends and family are and how lucky I am to have them in my life.

The other reason that I have had less time to blog this year is that I’m currently taking a distance-learning course in proofreading. I decided to take this course to get some more formal training in proofreading and also to learn more about the publishing industry as a whole. Excluding my PhD – which felt more like working than studying – this is the first course of study I’ve taken since I finished my undergraduate degree in 2009. It does feel a bit strange to be working on “exercises” and “assignments” again, but I’m really enjoying it so far.

I’m starting to emerge from the cloud that seems to have followed me around this year so I’m hoping to be able to blog more often. Watch this space.

How a virus gives back to its host

 

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Image by F_A (CC BY 2.0)

A study by UK scientists has shown that tomato plants infected with a virus are more attractive to bumblebees than healthy plants. Why would a plant virus want to change the behaviour of bumblebees?

The virus in question – cucumber mosaic virus (CMV) – can infect many different species of plant including tomatoes and a model plant called Arabidopsis thaliana. In tomatoes it causes many symptoms including yellowing, mottling, leaf distortion and can reduce the yield of seeds. As a result there is pressure for populations of plants to evolve better defences against the virus. Since CMV can only multiply within plant cells you might expect that, over time, CMV might become less common, but this doesn’t appear to be the case. One way the virus might be able to combat this problem is to compensate for the decrease in seed production in infected plants by encouraging pollinators, such as bumblebees, to visit the flowers.

Bumblebees fertilise tomato flowers by a process called buzz pollination, in which sounds produced by the bees shake the flowers to release pollen. Although tomato flowers can fertilise themselves without help from the bumblebees, buzz pollination makes the process more efficient and also leads to the transfer of pollen between flowers. Volatile compounds (molecules that easily become gases) released from the plants may help to guide the bees to the flowers. CMV infection can change the mix of volatile compounds that plants produce, but it was not clear whether this changes the behaviour of the bees.

Simon Groen, Sanjie Jiang, Alex Murphy, Nik Cunniffe et al. found that the bees are more attracted to the volatiles produced by CMV-infected tomato plants than those produced by healthy, uninfected plants. In the absence of buzz pollination, CMV-infected plants produce fewer seeds than healthy plants. However, mathematical modeling indicates that, in the “wild”, the bee’s preference for virus-infected flowers may help to compensate for this so that CMV-infected plants may produce more seeds than uninfected plants. Further experiments in A. thaliana suggest that molecules of micro ribonucleic acid (or miRNA for short) produced by the plants might regulate the mix of volatiles that plants produce.

These findings suggest that in some environments it may be in a virus’ interest to help its host plant by making the plant more attractive to bumblebees or other pollinators. Bumblebees are important pollinators for many crop plants so these findings may help us to develop new ways to increase crop yields in the future.

Reference: Groen SC, Jiang S, M, Murphy AM, Cunniffe N, Westwood JH, Davey MP, Bruce TJA,  Caulfield JA, Furzer O, Reed A, Robinson SI, Miller E, Davis CN, Pickett JA, Whitney HM,  Glover BJ, Carr JP. 2016. Virus Infection of Plants Alters Pollinator Preference: A Payback for Susceptible Hosts? PLOS Pathogens http://dx.doi.org/10.1371/journal.ppat.1005790

Bramble: friend or foe?

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Blackberries change colour from red to black as they ripen. Image by Thomas’ pics (CC BY 2.0 via Flickr)

In England at this time of year, the hedgerows along country lanes are full of delicious fruits called blackberries. Just last week I spent an enjoyable afternoon with friends gorging on blackberries along the route of an old railway line in Norwich (now a footpath and cycleway). The berries are a good source of vitamin C and antioxidants, and are commonly used in desserts and preserves. Although I love collecting and eating blackberries, I have a bit of a love-hate relationship with the plant that produces them, the bramble (Rubus fruticosus agg.).

Rubus fruticosus agg. isn’t a single species, but instead is a group (or aggregate; agg) of around 200-300 very similar species of shrub in the rose family that are very hard to tell apart (1). Like roses, brambles are covered in sharp thorns that help to protect the plant from herbivores (and humans). The thorns also help to make brambles a safe haven for many small birds and other wildlife.

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Brambles are pollinated by insects. Image by Roger Bunting (CC BY-NC-ND 2.0 via Flickr)

Brambles grow wild across most of Europe and in the UK they can thrive in most environments (1). The white or pinkish flowers are self-fertile and can still produce seeds even in the absence of fertilization (a process called apomixis) to produce an army of clone plants (2). Furthermore, brambles can produce suckers – new shoots from buds in the roots – which helps them rapidly cover an area of ground. As a result, brambles are often among the first plants to colonise abandoned plots of land. This is great for wildlife and the casual blackberry picker, but it’s not so helpful if you are trying to work on said piece of abandoned land…

When some friends and I took on an allotment this year, our plot had been neglected for a while and contained quite a lot of brambles. We removed a lot of the plants but have left some to be our own personal blackberry patch. Removing brambles is not a fun business as the thorns can cut through clothes (and gardening gloves). For several weeks in the spring my arms and legs were covered in scratches and I often found bramble thorns impaled in my fingers. If you don’t manage to completely remove the whole root, the bramble is quite capable of growing a fresh shoot so we’ve had a few cheeky brambles reappearing in the vegetable beds.

Despite my moaning about brambles I must say that the blackberry crop from the allotment has been great. It is kind of ironic that our most successful crop this year is something we weren’t deliberately growing. All in all, if I had to summarize my relationship with the bramble at the moment, I would say: “it’s complicated”.

 

References:

1) Wikipedia: Blackberry https://en.wikipedia.org/wiki/Blackberry

2) Brambles (Rubus fruticosus) http://www.woodlands.co.uk/blog/flora-and-fauna/brambles-rubus-fructicosus

Image links:

Bramble by Thomas’ pics

Canal: Morse to town 7 June ’11 by Roger Bunting

Poison in the garden

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The gates of Alnwick Poison Garden, north-east England. Image by Jacqui (CC BY-NC-ND 2.0) via Flickr

While giving my undergraduate class a tour of a botanic garden, a university professor said that “we should only eat the parts of a plant that the plant wants us to eat”. He was referring to the fruit, which many plants encourage animals to eat in order to spread their seeds in the environment (though not all fruits are edible). I don’t think he meant us to take his advice literally, but it is sensible to eat plants with caution. Alongside famous poisons including belladonna and hemlock, plants produce a variety of other molecules that aim to deter animals from eating them. Some of these molecules – such as ricin, which is produced by the castor oil plant – are so poisonous that tiny quantities can kill you. Others, like caffeine or the anti-malaria drug quinine, have less dramatic effects on the human body that we may find desirable or useful.

I recently visited The Alnwick Garden in north-east England, which has a special garden dedicated to educating visitors about the potential dangers of plants. In fact, some of the plants on display in the Poison Garden are so dangerous that visitors can only enter as part of a guided tour. I really enjoyed the tour and if you are ever in the area I recommend you pay the garden a visit.

The tour included some well-known poisonous plants, but the main message I took home from the tour was that many common garden plants are also potentially dangerous if they touch your skin or you accidently eat them. Below are a few examples of common plants that aren’t as benign as they might first seem:

Rhubarb (Rheum x hybridium)

While the pink fleshy stalks of the rhubarb plant are safe to eat and are commonly used in desserts, the leaves are highly toxic (1). This is thought to be due to the presence of high levels of oxalic acid, which can interfere with chemical reactions in the body by combining with calcium and other metals.

Common ivy (Hedera helix)

This rapidly growing vine is a haven for wildlife and attracts at least 70 species of nectar-feeding insects in its native range of Europe and Western Asia (2). Contact with ivy can cause an allergic skin reaction in some people, due to a natural pesticide in the leaves called falcarinol (3). Regardless of whether you are allergic to ivy or not, you should avoid eating this plant because its leaves contain saponins, which can cause vomiting, convulsions and even death.

Common nettle (Urtica dioica)

Children quickly learn that contact with common nettles results in a painful stinging sensation and skin inflammation. This is due to a cocktail of molecules including histamine, serotonin and oxalic acid, which is released from hairs on the surface of the leaves. For more information check out this cool infographic by Compound Interest.

Common laburnum (Laburnum anagyroides)

All parts of this small tree are poisonous, due to the presence of a molecule called cytisine, which has a similar structure to nicotine and has similar effects on the body. Laburnam is a member of the pea family and cases of laburnam poisoning are often caused by individuals mistaking laburnum seeds for peas and eating them (4). Mild cases may cause nausea and vomiting, but laburnum poisoning can also lead to insomnia, convulsions and coma.

These are just a few examples of common garden plants that can be harmful to humans and other animals. Fortunately, you can protect yourself against these and other poisonous plants by taking simple precautions, such as wearing gloves while gardening and carefully identifying edible plants when foraging.

Author’s note: Sorry for the long silence on this blog. My life has been quite chaotic in the last few months due to several events (expected/not expected, good/bad) and so the blog has had to take a back seat. Things are calming down a bit now so I’m hoping to get back into posting regularly, probably about twice a month. As ever, I’m always keen to receive guest posts so if you are interested in writing for Plant Scientist, please do get in touch.

References:

  1. The Poison Garden blog: Rheum x hybridium http://www.thepoisongarden.co.uk/atoz/rheum_x_hybridum.htm
  2. Wikipedia: Hedora helix https://en.wikipedia.org/wiki/Hedera_helix
  3. Compound interest advent calendar http://www.compoundchem.com/2014advent2/
  4. The Poison Garden blog: Laburnam anagyroides http://www.thepoisongarden.co.uk/atoz/laburnum_anagyroides.htm