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?

AmJBot explains Auxin to the perplexed

I’m delighted that there’s a review of Auxin in this month’s American Journal of Botany, Auxin activity: Past, present, and future by Enders and Strader. This might surprise a few of my friends as I’m not a fan of Auxin, Auxin is a difficult topic, and that’s why this review is so welcome.

Pink Perfection Camellia

Pink Perfection Camellia. Photo by Trish Hartmann. Construction by Auxin.

Auxins are hormones that are impossible to avoid if you’re studying botany. Sooner or later you’ll run into them. Recently in Annals of Botany they’ve been involved in inflorescence and floral organ development, adventitious rooting and xylogenesis, the growth of maize coleoptile segments and working with Arabinogalactan proteins in a paper with the best title I’ve seen in a while: Back to the future with the AGP–Ca2+ flux capacitor. AoB PLANTS is averaging a paper a month with an auxin influence this year to date (February).

What I find so confusing about Auxin is that it is everywhere, and it’s so well-known to botanists that it’s a necessary shorthand when writing a paper. This is great, but it makes papers featuring Auxin very difficult to read if you don’t already know about it. Enders and Strader cover a century of Auxin research for AmJBot and by placing Auxin research in a historical context, they help highlight how we know what we know about this very important hormone.

They start early with the quest to identify Auxin, but they highlight two key points in Auxin research in their review. One is the 1939 paper by Thimann and Schneider, The relative activities of different auxins. This pulled together what was known about Auxin, and helped clear some controversy. The other pivotal moment was adopting Arabidopsis as a model organism in the 1980s, and the associated advances of molecular biology that allowed experimentation with much greater resolution than before.

Like any good review there are plenty of links to other papers to read more, with major sections on metabolism, transport and signal transduction, but there’s also a helpful section at the end. Enders and Strader point to questions that are still open in Auxin research, like have all Auxins been discovered or are there still more to be found? There’s also an interview with Barbara Pickard on Kenneth Thimann which adds a human dimension to the research.

The impression I’ve had of Auxin research is that a lot of people have been finding out some really exciting stuff about the building blocks of plants. Reading one paper hasn’t turned me into an expert, but is has helped give me some idea about why people get so excited about Auxin.

You can pick up the paper free from AmJBot.

Find Article PDFs easily with Lazy Scholar

Looking to speed up your research? The Lazy Scholar extension for Google Chrome is now even more helpful.

Lazy Scholar Extension Page

I’ve mentioned Lazy Scholar before, but it’s worth mentioning again as it’s had an update. It’s an extension for Google Chrome that looks for PDFs of articles when you’re browsing abstracts. It also has some other nifty features.

You can search for papers by typing scholar.google.com into your address bar, then your search. With Lazy Scholar you can shorten this by typing ls search term which works as a direct search on Google Scholar for whatever you’re searching for.

The recent updates are easy paper sharing links and something else that looks useful: Lazy Scholar now checks Beall’s list of Predatory Journals. These are open access journals that will accept more or less anything, so long as you hand over the money. I have seen one or two good authors publish papers in predatory journals, but Lazy Scholar now adds a warning to let you know that what you’re looking at is a questionable journal.

If you use Chrome during your research then it’s well worth downloading Lazy Scholar from the Chrome Web Store (for free).

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?

Why would a plant make its pollination less efficient?

The special issue on pollinator-driven speciation is available with free access now. We covered a few of the papers last year, but now they’re all free. One of the more puzzling papers is Novel adaptation to hawkmoth pollinators in Clarkia reduces efficiency, not attraction of diurnal visitors by Miller, Raguso and Kay. Why would a plant make its pollination less efficient?

Miller et al. look at the effect of novel pollinators. If new pollinators arrive, or plants move into an area with pollinators they’ve not encountered before, there’s a resource to exploit. They looked at Clarkia concinna and C. breweri which have parapatric distributions. Parapatric wasn’t a word that I knew so I had to look it up. They’re species that live next door to each other without overlap.

Clarkia flowers

Different functional groups show different efficiencies on C. concinna (left column of photos) and C. breweri (right column). (A, B) Small bees either collect pollen or nectar at the opening of the hypanthium tube. With both foraging behaviours, they frequently contact the stigma of C. concinna but rarely contact the highly exserted stigma of C. breweri. (C, D) . Photo by Miller et al.

C. concinna and C. breweri get different visitors. Miller et al. wanted to find out what it was that caused this difference. Was it the different ranges the plants live in, or was it floral differences? So they examined visits to arrays of the plants and also created arrays that had the two species of plant at a shared location. They could then see if the flowers from one species were more attractive to certain pollinators than another.

What they found was that diurnal visitors were happy to visit both plants. Even hawkmoths were happy to visit C. concinna even though it looked like C. breweri had evolved traits to attract them. The difference was due to pollinators in different ranges. Puzzle solved.

However, this opens another problem. If C. concinna and C. breweri share the same visitors, how could the differentiate? They could swap pollen so there should have been gene flow between the populations and so no divergence. Miller et al. cut through this by reducing the effectiveness of flowers down to two attributes. Attraction is one, the flower has to get the pollinators to visit. The other is efficiency, once there the flower has to get the pollinator to carry the pollinator away.

C. breweri might pull in many visitors, but the ones that really work are the hawkmoths, thanks to the adaptations it has made. The hawkmoths could visit C. concinna but they weren’t so successful in depositing pollen. It’s no surprise then, given the issue the paper is in, that it seems that it’s the effectiveness of the pollinators that seems to be driving differentiation.

Graph showing how hawkmoths are more efficient for C Breweri.

Two measures of hawkmoth pollinator effectiveness. (A) Total visits to Clarkia breweri and C. concinna in choice trials. Hawkmoths visited both species equally (P = 0·41), but successfully probed C. breweri more (P = 0·052), and approached C. concinna without probing more (P = 0·012). (B) Number of pollen grains deposited on the stigmas of both species per probe in single species pollen deposition trials. Hawkmoths deposited more pollen per visit on the stigmas of Clarkia breweri than Clarkia concinna (P < 0·001). Error bars, ±1s.e. From Miller et al.

It also shows some of the complexity of evolution, including that the premise of question is wrong. Often simple explanations of evolutionary changes are that a plant changed something in order to…. This is an simplification because teleology doesn’t work in evolution, plants don’t do something in order to get a future pay-off. Likewise Miller et al. show that Clarkia didn’t change to attract new pollinators, more that once new pollinators are available there’s an advantage to work better with those. In the case of Clarkia natural selection worked in favour of plants that could use hawkmoths, and once that happened the descendants became less able to swap pollen with the older population. Instead they tended to swap with each other, until the differences were so great they were a new species.

The key here is the difference ranges of the Clarkia species. It’s not simply that they’ve attracted a new pollinator, they’re not in a position to attract the pollinators of their ancestors. Miller et al. point out that the situation for species that share the same patch will be different. When examining pollinator-driven speciation, it’s not simply a matter of attraction, they argue but also a matter of availability of novel-pollinators and the quality of those visits.

Miller T.J., Raguso R.A. & Kay K.M. (2013). Novel adaptation to hawkmoth pollinators in Clarkia reduces efficiency, not attraction of diurnal visitors, Annals of Botany, 113 (2) 317-329. DOI: http://dx.doi.org/10.1093/aob/mct237

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.

Snacking helps Drosera’s appetite

A paper by Pavlovič et al. has caught my eye this week. Feeding on prey increases photosynthetic efficiency in the carnivorous sundew Drosera capensis has moved into Free Access. I’m used to the idea that carnivorous plants trap insects to get Nitrogen, but it is a bit more complicated than that.

Drosera capensis

Drosera capensis

Pavlovič et al set up an experiment to follow the feeding cycle of D. capensis. D. capensis is a sundew, it eats insects by trapping them on sticky leaves, coiling round them and then secreting enzymes to digest the insect. Its home is South Africa, but it’s commonly cultivated around the world now.

Pavlovič et al. were testing a simple idea. What benefit does a plant get from feeding, and how can you measure it? Givnish et al. said feeding led to increased photosynthetic efficiency. So the experiment looked at gas exchange and chlorophyll a fluorescence. They also examined what enzymes get released by the sundew to see what it is that the plant is most eager to get. They also tried another experiment which worked, but didn’t get spectacular results.

D. capensis has another form. If you don’t want red tentacles on your plant you can now buy Drosera capensis alba, a plant with white tentacles. Pavlovič et al. wondered if red, found in the wild, was a signal to attract flies. The experiment they did to find out is the simplest. Get some fruitflies, put them into tanks with sundews with the two varieties and then see which plants catch most.

What they found was there was no significant difference. This doesn’t mean the experiment failed, instead it tells us that there is no preference and whatever reason there is for the red, it’s not to attract insects. It might sound dull, but it means something odd is happening. It’s not just sundews that are red. Various forms of Nepenthes and Sarracenia also grow red forms. Yet it doesn’t seem that these use red to attract insects either, so why are various carnivorous plants coming to the same colour?

As far as digestion goes, Pavlovič et al. found that all it takes for sundews to release enzymes is some mechanical stimulus, and they found this when they used polystyrene balls as well as flies. However, to really get digestion happening the plant seems to need more poking, like from a live insect and some chemical feedback. Obviously they weren’t getting this from the polystyrene balls.

When it came to seeing what the leaves were pulling out of the insect there was a mild surprise. Nitrogen and Phosphorus were obvious grabbed along with Potassium. They did not see absorption of Calcium or Magnesium, despite other people finding Mg take-up in other experiments. Pavlovič et al. think that their plants may have already had a relatively high Mg concentration.

The key input for Drosera was Phosphorus. Pavlovič et al. found their unfed plants were P-limited, meaning that it was a lack of Phosphorus that stopped them from growing as well as they could. Phosphorus is essential for making ATP, Adenosine triphosphate, which powers plant cells and is a key part of respiration. Without Phosphorus, plants would not be able to photosynthesise, so while it’s a small part of plant’s chemical make-up it is still very necessary.

The paper is good for what it finds, I like seeing how the nutrients are tracked so you can see the plant using them, but the referencing is important. This isn’t isolated research, it builds on other work and it’s contributing to a conversation. The authors don’t just include references to support them. The lack of Mg absorption by the sundew leaves is a puzzle, but Pavlovič et al. point to the papers that show this in order to put their own results in context. That is the best way of showing how new research can help expand the field more.

Pavlovic A., Krausko M., Libiakova M. & Adamec L. (2013). Feeding on prey increases photosynthetic efficiency in the carnivorous sundew Drosera capensis, Annals of Botany, 113 (1) 69-78. DOI: http://dx.doi.org/10.1093/aob/mct254

The most efficient trap isn’t always the most deadly trap

Pitchers plants are carnivorous. They catch small animals, usually insects to gain nutrients like Nitrogen. You’d expect that they’d evolve their traps to be as effective as possible. If an insect gets away, that’s one less meal, but that’s not what happens for Nepenthes rafflesiana

Nepenthes rafflesiana. Photo by i-saint/Flickr

Nepenthes rafflesiana. Photo by i-saint/Flickr

N. rafflesiana is a plant that grows in sunny parts of the forests of Borneo, Sumatra, and the Malaysian peninsular. It grows a couple of traps, though the upper traps lack the waxy crystals of the lower traps. Both traps have a peristome, a lip that is very slippery when it’s wet to encourage insects to fall in. But often is isn’t wet. In fact the change in humidity through the day means that it can be dry for eight hours or more. Dr Ulrike Bauer from Bristol decided to have a closer look at what was going on.

She and her team examined plants in Brunei, in the north of Borneo. At first they examined the traps of plants to see how they worked normally. They found the plants ate ants. They ate other things too. There were a few termites, along with some bees, beetles and spiders, but the bulk of food was ants in young pitchers.

Experimental set-up for Pitcher plants

Experimental set-up to test the effect of constant wetting on ant recruitment and trapping. On each N. rafflesiana plant, two pitchers were prepared in this way but only one pitcher per pair was connected to the water supply. Wetted and control pitchers were swapped halfway through the experiment. Image by Bauer et al. 2015.

Next she tried something simple but clever. She rigged up some pitchers so that they were moistened by a drip from a bottle. The aim was to find out if the peristome drying out during the day badly affected the plant’s ability to capture ants. Each ‘wet’ pitcher on a plant had a companion ambient pitcher rigged up in the same way – to counter the effect of the equipment. Half way through the experiment the pitchers were switched so the ambient pitchers were moistened and the wet pitchers left to dry in the ambient environment.

They found that wet traps captured more flies, so it seems that a wetter trap is more deadly. So do the traps drying out indicate a plant at the limit of it’s range? Maybe slowly becoming more deadly? Bauer thinks that something different is happening, the pitcher plants are using ant behaviour against the ants.

Ants search for nectar, which makes the pitchers effective traps. But if you kill an ant that visits you have just one ant. If that ant can go back home and bring her friends back then you have a party of ants coming to your trap. Bauer et al. found that traps were making batch kills, which suggests this is what’s happening. It’s a good explanation, but it bothered me. They also point out that mass kills are comparatively rare events. That’s fine if you have lots of traps, but a bigger gamble if you have just a few. However, Bauer et al. have an answer for that.

As I mentioned above N. rafflesiana doesn’t produce just one kind of trap. The lower traps have waxy crystals, so while the peristome isn’t always effective, the wax means the lower traps are always working. Young plants are close to the ground to begin with, obviously, so they start by building conservatively with always-on traps and then build more effective batch-kill traps when they can afford to play a longer game.

This is the kind of science I like. The basic idea is simple and easy to explain, but it still takes observation and some careful thought to work out what the observations are telling you. You can also tell that Bauer and her co-authors are confident of their findings, because the paper is written in a way that’s easy to understand. The fact they’ve found the most deadly trap isn’t always the most efficient trap is a bonus.

You can pick up the paper for free, it’s Open Access, at Proceedings of the Royal Society B.

Bauer U., Federle W., Seidel H., Grafe T.U. & Ioanou C.C. (2015). How to catch more prey with less effective traps: explaining the evolution of temporarily inactive traps in carnivorous pitcher plants, Proc. R. Soc. B, 282 (1801) DOI: http://dx.doi.org/10.1098/rspb.2014.2675

Deadly competition between parasites

There’s an interesting paper out in Nature Communications: Coinfection alters population dynamics of infectious disease. The paper is the study of Plantago lanceolata a common weed where I live in the UK. It’s found across Europe to India and Africa, and as an invasive plant in North America, China and Australia. It’s an example of why scientific names are so important, because I’d call it Plantain, but it’s nothing like the plantains that people eat as Musa.

P. lanceolata is host to a mildew, Podosphaera plantaginis. It looks like a white powder on the leaves of plants. In fact it’s burrowing roots into the leaf and growing spores to spread elsewhere above it. The parasite is not good for the plant, but it needs a live host to survive. Yet sometimes infections take a turn for the worse. What causes that?

The key is co-infection. Sometimes multiple strains of parasite infect a plant. When that happens things get much more complex. With a simple infection, the parasite only needs to overcome the plant. However, if a plant has multiple parasites, then they compete with each other. Normally a gentle approach would be enough for a parasite, but when there are multiple infections then a more aggressive attacker can pull resources from its competitors. At least that’s how you’d expect it to work.

To find out if it’s true Anna-Liisa Laine and her team based at the University of Helsinki carried out experiments and field surveys in the Åland Islands, southwest of Finland. This is part of a longer-term study on infection, so they had well-known plant populations to examine. In September (2012) they took a leaf from up to 10 plants per population and examined the DNA. They also infected leaves in the lab, and in garden plots.

I think the most striking result they got is in the graph below. The bars measure spore activity, and green and blue bars measure infections from single strains of mildew. The red is what you find when there’s a coinfection.

Coinfection increases spore activity

Singly inoculated plants shown in blue and green and co-inoculated plants in red. (a) Mean number of spores caught on microscope slides from singly inoculated (3=green and 10=blue) and co-inoculated (red) plants. (b) The proportion of live leaf traps that became infected. Error bars are based on s.e.m. Image by Susi et al.

Anna-Liisa Laine, who led the project said: “Here we find that coinfection by different strains of the same pathogen species completely change infection dynamics. These results are really just scraping the surface of how complex infection dynamics can be under coinfection. In our current work we’ve discovered that ribwort plantain populations in Finland contain hundreds of viruses. We’re now measuring how this within host disease community affects infection dynamics for a wide range of pathogen species.”

You can pick up the paper as an Open Access publication from Nature Communications.

Susi H., Barrès B., Vale P.F. & Laine A.L. (2015). Co-infection alters population dynamics of infectious disease., Nature Communications, DOI: http://dx.doi.org/10.1038/ncomms6975