All posts by Alun Salt

About Alun Salt

When he's not the web developer for AoB Blog, Alun Salt researches something that could be mistaken for the archaeology of science. His current research is about whether there's such a thing as scientific heritage and if there is how would you recognise it?

A new website introducing genetic engineering

The Journey of a Gene is a new website at UNL-Nebraska that teaches the basics of genetic engineering. There’s a combination of videos, some from YouTube and some specifically made as well as some interactive sections.

The video above, explaining what a gene is, is an example of what they’re bringing in. Later they explain the role of promoters and coding and you get elements like the video below explaining how to use the interactive elements.

I tend to be wary of websites a teaching tools by themselves. There are very few good ones. However, I don’t know if they have some sort of special unit at UNL, but this is the second time I’ve found useful interactive animations produced there. They also do some handy astronomy tools. As one of AoB Blog’s non-botanists, I found the videos genuinely helpful in explaining some of the genetic engineering process.

It’s hard to say why some sites work and some don’t. If it was easy to spot why something was rubbish, then it’d be easy to fix. In this case, I think building it around one specific problem, Soybean Sudden Death Syndrome, means that you have an idea of what the context is. It’s not just random information; there’s actually a point to it. That kind of narrative structure means that the sections follow on from each other in a sensible way.

If you’re a new student and want a little extra help getting your head around what a gene is, and how DNA inheritance works when you start crossing and backcrossing plants, then you should definitely give the site a go. I can’t guarantee you’ll be genetic engineering your own plants by the end of the course, but you might at least have a better understanding of how it happens.

A tip o’ the hat to Agriview for pointing me at this.

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Stevia hits the mainstream with ‘Life’

Last year AurĂ©lien Azam blogged about Stevia in his post, Can we find all the tastes we like in the Wild? He mentions Stevia in it and if you don’t remember it, then Coca Cola will try to change that. Stevia is the plant behind the new Coke variety, Life.

Coca Cola Life and Death

The marketing department at Coca Cola are about to discover that if the green bottle is called ‘Life’ there’s an obvious name for the red bottle.

Stevia rebaudiana leaves are complicated sugar factories. Initially they import carbohydrates, but as leaf area increases photosynthesis means they start producing more sugars to supply the rest of the plant. The key chemicals are Steviol glycosides. These are, for the same concentration, around 300 times more sweet than sugar. The exciting feature is that human body cannot produce any calories from these sugars. For marketing, it’s the fact that it’s a plant that’s the chemical factory that’s news. If it’s made in a plant then you can label it: From Natural Sources.

But this is one of those situations where natural is probably not a synonym for good.

Stevia growing naturally in Paraguay. #156515950 / gettyimages.com

Abdel-Rahman et al. (2011) report on Stevia, among other natural products in Toxological Sciences, and note that in aqueous, crude or partially purified form Stevia can be bad news for rats. One side-effect can be reduced fertility in female rats. It’s always best to be wary from directly applying animal tests to humans, but they also note that the Guarani Indians of Paraguay would make something a bit like a tea from the Stevia leaves. They used it as an oral contraceptive.

For this reason it’s a relief that the sweetener isn’t natural, but a highly processed form of Stevia. But how does it taste?

I set up a comparison taste test with Coca Cola Life (green bottle) and the Cola Cola from the red bottle – which for ease of labelling we’ll call Death. I also added Coke Zero as a third option. All bottles were chilled and the opened with ice added. I then ignored protests from the tasters that they weren’t that thirsty.

The taste test followed a predictable pattern.

After glass 1 Zero: “Hmm.”
After glass 2 Death: “That’s definitely the full-fat Coke and the first is Stevia.”
After glass 3 Life: “Euww! No, that’s Stevia isn’t it?”

Stevia has a distinctive taste, and one that’s unexpected in Coke. Success will depend on how much the public develop a taste for it.

If it does succeed, the payoff could be big. As well as the battle against obesity, Stevia-derived sweeteners promise other benefits including fighting diabetes, high-blood pressure and tooth decay. However for now if it’s a choice between liberty from health issues or Death, a good chunk of the public will opt for Death.

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The hidden cost of frankincense

A while back we covered a paper in Annals of Botany on tapping frankincense for resin. The mapping of the canals in the tree promised to improve the efficieny of tapping. Now in Tree Physiology Mengistu et al. have a paper Frankincense tapping reduces the carbohydrate storage of Boswellia trees, that’s recently become free access.

Boswellia Trees

Boswellia Trees in Ethiopia. Photo by Motuma Tolera.

Mengistu et al. show that tapping for resin reduces the trees’ stores of starches and sugars. They also show that stores deplete anyway, as the tree uses them itself. The resin is part of a store that tides the tree over the dry period, and get replenished during the wet period.

The paper ties in well with the Annals paper. In that Tolera et al. argued resin tapping could be done just as effectively with fewer cuts. Fewer cuts means less chance for disease to enter the tree. In the TreePhys paper Mengistu et al. argue that fewer cuts also means that trees have more of a chance to hold on to necessary stores of carbon, if they need them.

The evidence is that intensive tapping of Boswellia papyrifera is a problem and that the trees need some respite. However, there is also a religious imperative to tap them. Balancing supply and demand looks likely to remain a contentious problem.

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Does Plant Science need a Sagan or Sheldon?

Here’s a slow reaction to a post at ASPB Plant Science Blog by Ian Street, Communicating Plant Science in the Digital Age. It’s taking me a while to respond, because I think it’s a good post – but I don’t quite agree with it. However, every time I think I’ve worked out why I don’t agree with it, I find I don’t agree with myself either.

In the original post, Ian Street holds up Neil deGrasse Tyson as an example of someone who is an excellent communicator and points out there’s no plant science equivalent. Here I start to feel a bit of a weasel. In terms of audience and fame he’s right. However, if you’re looking for people who can communicate plant science in an exciting way, there are plenty of researchers who could do a similar job to Tyson, given the opportunity. I think there are plenty of good communicators in botany, but they don’t have the audience.

I can see why not having a Plant Tyson is a problem, but I’ve not been sure that broadcasting is the answer. I don’t think astronomy is popular because Tyson is a good communicator. I think it’s the opposite way round. Tyson is such a good communicator because Astronomy is so popular. That might sound odd, but imagine if Tyson decided he’d had enough and was retiring to Tahiti, would Astronomy cease to be popular?

No. There’s a demand for astronomical talking heads. There’s someone almost as good who could do the job. The demand for popular astronomy means there’s almost certainly a pool of talented communicators that the media could draw upon. Tyson is at the top of a competitive field. There are plenty of talented plant science communicators, but lack of demand means we con’t see them so much.

I think a top plant science broadcaster lies at the end of the road to making botany more popular, it’s not part of the journey itself.

Sheldon Cooper

Is CBS’s Sheldon Cooper the face of Science in the 2010s?

That works as far as it goes, but elsewhere I think Ian Street proves me wrong and gives an example where broadcasting does work. He mentions The Big Bang Theory that, love it or hate it, humanises physicists.

In the UK it’s been credited with an increase in the number of physics students. For a similar effect see archaeology and Indiana Jones. You can’t learn physics from The Big Bang Theory any more than you can pass a course in archaeology with Indiana Jones – but the lack of facts hasn’t prevented them from changing how people value their respective sciences.

Street also points out the importance of using comedy to take the edge of hard science. I think he’s hit on a key point there. It’s not simply a matter of making plant sciences prestigious, you also need to make them likeable. Yesterday we had a post on a genetically engineered plant that might help fight Ebola. It’s a huge tragedy where plant science could make a major contribution to saving lives. But I’m also willing to bet that anti-vaxxers will decide it’s a secret Monsanto project.

In a perfect world Hollywood would solve the image problem for us, but that’s not a practical solution. So instead of aiming for mass audiences, it might be more reasonable to look to the small things people can do. Ian Street says that popularising science is a core part of scientists’ mission. This may be a culture difference, but in the UK it is emphatically not. The only things that matter are scientific publications. Departments make positive noises about outreach, but when it comes to assessments time spent doing Outreach can be viewed as Time Not Working.

If outreach success is all-or-nothing, then in this situation the vast majority of results are going to be nothing. If there were support for small victories, then hopes need not rest or a Sagan nor a Sheldon. Avoiding investing in a few personalities could have benefits. Not least, because it means scientists don’t have to just look like me, they can look like you and your neighbour too.

Quite how this is going to be put in place is difficult, but I think what Ian Street and the ASPB’s Digital Futures Initiative might well be a stepping stone to support for many plant scientists. Another event to cheer is Kevin Folta, who’ll be doing a Reddit AMA this afternoon.

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It’s fruit Jim, but not as we know it

There’s an interesting paper we’ve just moved to free access: Gymnosperm B-sister genes may be involved in ovule/seed development and, in some species, in the growth of fleshy fruit-like structures by Lovisetto et al. The idea that seeds are associated with fruits should be no surprise. Animals eat the fruits and disperse the seeds, so the plant can spread its genes. Fruit from gymnosperms would be a surprise though, because you’d expect the fruit to grow from a flower and gymnosperms don’t have flowers, those are angiosperms.

However, the cover image for the August 2013 Annals of Botany shows ovules of Gingko biloba that grow a fleshy structure that attracts animals. What’s going on?

Ginkgo biloba

Ovules of the gymnosperm Ginkgo biloba. Image by Lovisetto et al. 2013

The answer seems to be in the genes. Both angiosperms and gymnosperms have B-sister genes that work to grow fruit. It looks like the foundation of growing fruit around a seed could pre-date the development of flowers.

You can read more free at Annals of Botany.

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One plus one does not always make two, when plants add up costs and benefits

Mutualism is a relatively simple concept in plant science. Plants will reward other organisms that perform services for them, so both the plant and partner are better off then they would be alone. But what happens when you add more than one species to an ecosystem? Non-additive benefit or cost? Disentangling the indirect effects that occur when plants bearing extrafloral nectaries and honeydew-producing insects share exotic ant mutualists by Amy Savage and Jennifer Rudgers shows it’s not always as simple as adding up costs and benefits to find out the net effect species interaction has.

Being simple myself, the phrase ‘non-additive’ puzzled me, but there’s an excellent graph that explains what Savage and Rudgers mean. They think of a plant hosting two species. One is an ant. The ant tends to protect the plant from herbivores – except one. The second species is a sap-sucking insect that produces honeydew, a sugary substance that’s a bit like an insect’s version of nectar. What happens if you put the two species on a plant?

The Additive model simply adds up costs and benefits. So if ant protection boosts growth by two units, but the sap-suckers deplete it by one, then the net benefit is one unit to the positive. That’s the first graph below. But it might not be that simple.

Cost and Benefit models by Savage and Rudgers

Cost and Benefit models by Savage and Rudgers 2013.

Ants like honeydew, because of the complex sugars. But suppose ants REALLY like honeydew. So much that hosting the insects pulls a massive number of ants up to protect the leaf. Here is what is called a Non-additive benefit model. The next effect is far more positive than simply adding up the interactions of the two species with the plant. But this could go the other way too. Maybe the protection given by the ants really allows the sap-suckers the safety to plunder the plant. Then you have a Non-additive cost model – the third graph.

It turns out there hasn’t been much research on the combined effects of ants and honeydew producing insects (HPI) on plants. This is an issue because of another complex factor – what happens when one ant invades the territory of another?

Savage and Rudgers looked at ants on Savai’i, Samoa, in particular Anoplolepis gracilipes. A. gracilipes correlates with extra-floral nectaries on plants, and is more aggressive to other insects on its patch than other ants. The mutualism between A. gracilipes and plants could be aiding A. gracilipes kill off other insects in the area.

Samoa in the Pacific Ocean

Image from Google Maps.

The study was on the lava flows of Savai’i, colonised by Morinda citrifolia a plant with floral, extrafloral and post-floral nectaries. It produces nectar all year round. They picked a variety of sites, some with A. gracilipes and some with less invasive ants present.

To test the effects of the ecological interactions they could remove ants from plants, by circling the base of a plant with a pest barrier. They could reduce nectar production by bagging the nectary bodies. They could also reduce the presence of HPI by brushing them off the plants. They could then manipulate some of these factors together.

For A. gracilipes, they found the key was nectar. Reduce nectar and you reduce the number of ants on the plant. Reducing HPI only had a small effect, which suggests A. gracilipes aren’t so bothered about honeydew.

For the plants, the presence of the ants makes a big difference. They hardly grew without any A. gracilipes around, but grew 3000% with the ants around. HPI had little effect without A. gracilipes, but also promoted growth then there were ants there too. This supports a non-additive benefit model. For the less invasive ants the effect the effects were less than additive.

One of the interesting findings was that the A. gracilipes had an effect on HPI, turning them from a negative to a positive for plant growth. It’s something that you could not predict simply from observing just A. gracilipes or HPI. The paper certainly provides plenty to think about on the complexity of cost and benefit analysis. You can now pick it up for free from Annals of Botany.

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Floating Forests brings Plant Science to YOU this summer

Do you fancy doing plant science off the shores of Tasmania, around the Antarctic, or even Hawaii? Then the Zooniverse has the project for you. Floating Forests is a website to study the growth or decline of giant kelp, Macrocystis around the world.

Floating Forests

Giant kelp is pretty well named. It can grow to sixty metres in length and it is found around the world. The undersea forests they make are vital habitat for many other species. So tracking growth or decline would be a good thing. The difficulty is that you simply cannot dive everywhere to examine the forests up close – and this is where the Zooniverse comes in.

The Zooniverse site was set up to have the public classify galaxies at a site called GalaxyZoo. Astronomers knew humans were much better at recognising what sort of galaxies they were looking at than computers. The average member of the public wouldn’t be as good as a professional astronomer, but ask enough and you can average out all the errors and get a result better than one professional classifying galaxies. They also found you got results faster, because there’s plenty of people willing to help with primary science.

Floating Forests works in a similar way, but instead of looking out from Earth to space, the Floating Forests images are taken from orbit looking at Earth.

To take part you first sign up. Then you can see a tutorial on how to mark up images, but it’s basically drawing loops around what you think is kelp.

Your eyes might be better than mine, and you might see more kelp in the images. Or maybe I was trigger happy and marked too much. Averaging will help factor out mistakes similar to the concept of The Wisdom of Crowds.

The images are from Landsat. It means the any individual image could be lousy. There are corrupted images, some which are just land or sea and plenty that are clouded out. They have tools for working round this. The upside of using Landsat data is that there’s an archive going back thirty years, so while a place might be clouded out one month, it’s not likely to be covered all the time. It opens the potential for detailed analysis by season and over time.

The project is a collaboration between the Zooniverse and the Kelp Ecosystem Ecology Network, and they’re running a blog to keep people up to date with what they’re finding. The Zooniverse has been terrific in getting people engaged with astronomy. With luck, KEEN can do the same for marine ecology.

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Plant Science around the web…

Links

The Indian Botanists have a review of ‘Green Wars- Dispatches from a Vanishing World’ by Bahar Dutt as well as an interview with her about the book.

Bibliodyssey, the art history blog, has a post on pomology and some illustrations from the 19th century.

Via Anne Osterrieder, there are the most well-referenced Frozen parodies I’ve seen, with New Under The Sun Blog’s post, Do you want to make a plastid? and For the First Time in Forever: Vernalization

I’ll assume you’ve already seen the Agricultural Biodiversity Weblog’s Nibbles.

Photo: BigStockPhoto.

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Sweet nectar gives ferns a bitter taste

A collection of papers on Extrafloral Nectaries has recently moved into Free Access at Annals of Botany. One of the papers raises the question, can a plant that never flowers have extrafloral nectaries?

An unwanted caterpillar

Photo: Koptur et al.

Nectar secretion on fern fronds associated with lower levels of herbivore damage: field experiments with a widespread epiphyte of Mexican cloud forest remnants by Koptur et al. examines why ferns produce nectar. The paper starts with a brief review which includes a few facts that startled me. One is that extrafloral nectaries evolved before floral nectaries. This surprises me because I so deeply associate nectar with flowers. Another shock was that nectaries appear on ferns well before ants appear in the fossil record.

This shouldn’t be a surprise, but we’re so used to evolutionary stories being teleological, like plants evolved nectaries to reward insects, that it’s easy to forget that it’s a huge oversimplification that gets things very wrong. Nectaries didn’t evolve in order to do something with a purpose. Instead that plants with nectaries have a better chance of passing their traits to their offspring because they can reward insects. And what if there are no insects? Koptur et al. say that the early appearance of nectaries supports the ‘leaky phloem’ hypothesis, that sugars are forced out of the plant in weak developing tissues to ease hydrostatic pressure in the plant. This might explain how they formed, but once ants arrived did they help select ferns with better nectaries. Do the nectaries in ferns given them an evolutionary advantage?

The nectaries are on the leaves or fronds of the plant. Developing fronds are a prime target for herbivores, so if the ants were drawn into the leaves they could act as a defence. But do they. The experiment, like many of the best ones, sounds quite simple.

At its simplest, you find a plant with a suitable pair of young fronds. On one you paint over the nectaries with nail polish to prevent access to the nectar. You then see how the plants develop and compare the damage on the untreated leaf with the test leaf. Reality is messy, so they actually did a lot more than that to account for other factors – but the basic experiment was does access to the nectaries matter?

The results were clear. The fronds with blocked nectaries had four times the damage of the untreated fronds. The ferns benefited from hosting plants, and the ones that could attract them best got the best defence. The defence works best against invasive species that haven’t co-evolved with the fern and developed counter-defences against the ants.

It’s easy to see nectar as part of the plant’s reproductive strategy, or maybe as part of the reproductive system that’s been repurposed for something else. I think this paper neatly shows that there’s no need to assume any connection at all. There’s a lot more to nectar than bait for pollination.

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