Monthly Archives: November 2011

In search of the Platzgeist (TIME 100)

It’s easy to pin scientific credit on a person. He or she usually has a name on the key publication, but how do you credit a place? Science is a human activity, so is it just the humans that matter or are there things were place contributes as much as people? While I was kicking round this idea, Pat came up with a few places that he thought mattered.

Mendel's garden in St. Thomas's Abbey, Brno.

Mendel's garden in St. Thomas's Abbey, Brno.

The first website he pulled up was Biodiversity Hotspots. I’d never seen this before. It’s fascinating. I didn’t know the Irano-Anatolian region was a biodiversity hotspot. I’m more familiar with it from the development of early crops that eventually led to agriculture spreading across Europe. In terms of plant-life this is a disaster in progress. Orchid collection is threatening species throughout the region. Other eyecatchers are the halophile plants that have adapted to live the extremely salty conditions rendered hot and dry by the sun. There’s plenty of the site to look at, but I couldn’t find Mauritius listed.

I can’t work out whether Mauritius is a good choice or not. It’s an ecological catastrophe in progress at the moment, but there’s a lot of work saving species going on with tiny budgets. Work in Mauritius could make a difference around the world. Douglas Adams identified it as the place where humans first recognised they could make a creature extinct, when the last dodo was killed and there were going to be no more dodos ever. On his visit he also wrote the most amusing description of the near extinction of a plant.

We finally made it to Rodrigues, a small island dependency of Mauritius, to look for the world’s rarest fruitbat, but first of all we went to look at something that Wendy Strahm was very keen for us to see – so much so that she rearranged her regular Rodrigues-visiting schedule to take us there herself.

By the side of a hot and dusty road there was a single small bushy tree that looked as if it had been put in a concentration camp.

The plant was a kind of wild coffee called Ramus mania, and it had been believed to be totally extinct. Then, in 1981, a teacher from Mauritius called Raymond Aquis was teaching at a school in Rodrigues and gave his class pictures of about ten plants that were thought to be extinct on Mauritius.

One of the children put up his hand and said, ‘Please, sir, we’ve got this growing in our back garden.’

At first it was hard to believe, but they took a branch of it and sent it to Kew where it was identified. It was wild coffee.

The plant was standing by the side of the road, right by the traffic and in considerable danger because any plant in Rodrigues is considered fair game for firewood. So they put a fence round it to stop it being cut down.

Immediately they did this, however, people started thinking, ‘Aha, this is a special plant,’ and they climbed over the fence and started to take off little branches and leaves and pieces of bark. Because the tree was obviously special, everybody wanted a piece of it and started to ascribe remarkable properties to it – it would cure hangovers and gonorrhoea. Since not much goes on in Rodrigues other than home entertainments it quickly became a very sought-after plant, and it was rapidly being killed by having bits cut off it.

The first fence was soon rendered useless and a barbed wire fence was put around that. Then another barbed wire fence had to be put around the first barbed wire fence, and then a third barbed wire fence had to be put around the second till the whole compound covered a half acre. Then a guard was installed to watch the plant as well.

With cuttings from this one plant Kew Gardens is currently trying to root and cultivate two new plants, in the hope that it might then be possible to reintroduce them into the wild. Until they succeed, this single plant standing within its barbed wire barricades will be the only representative of its species on earth, and it will continue to need protecting from everyone who is prepared to kill it in order to have a small piece. It’s easy to think that as a result of the extinction of the dodo we are now sadder and wiser, but there’s a lot of evidence to suggest that we are merely sadder and better informed.

Last Chance to See, the book of the radio series.


It’s that last sentence that’s the problem with Mauritius. The dodo might be extinct, but has the extinction really changed anything? At the moment the rate of extinction is climbing, so it seems not.

Another place Pat suggested was St Thomas’s Abbey in Brno. This was where Mendel performed his experiments on peas. The cleverness of Mendel is in no doubt, but is the Abbey special? Could the work have happened elsewhere? It’s an unanswerable question, but it’s worth recognising the opportunities and demands that the abbey placed on Mendel would be very different to a university post. If you follow the extended mind hypothesis, is a place part of the cognitive process? There’s also a question of whether a connection needs to be that deep to be historic. Is it enough that something happened here first to make it noteworthy?

As an example of a place where ‘it happened here first’ might be enough, there’s Botany Bay in Australia. New Holland was known long before Cook’s arrival. The expedition in the South Seas had found many more plants and animals before landing at Botany Bay. Banks was a good botanist, but if another competent botanist had been on the trip they could have spotted the flora was different. The ship didn’t even need to arrive at that specific point in Australia to produce an event. If they’d landed a bit further north, there still would have been a shore of unseen plants. So if the botanist and place are interchangeable what is the attraction? I think it is entirely ‘it happened here first’. The contact event could have happened anywhere along the east coast but here is where it happened. It’s what encouraged the British government to start transporting convicts and even though Botany Bay was not a successful site (the settlement had to move to Sydney) it was the thing that pulled British colonisation into the region.

Clearly for Botany there are places that are simply special. Pat also mentioned the Last Stand of the Wollemi Pines as an importance place in Botanic History, though probably not quite as dramatically as that. Plants can make a place important but the possibility of a Platzgeist something like a spirit or an atmosphere of a place, like a zeitgeist situated in space rather than time, that makes a discovery in one place possible while it’s not in another is interesting – if I could define it in less vague terms.

Photo: Jardín donde trabajó mendel en Brno by Rafael Robles. Licenced under a Creative Commons BY licence.

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Education and Research of Plant Breeding for the 21st Century

General Perspective

Many jars on shelves in a seedbank.

A seedbank of crop germplasm: The analysis of genetic variation in germplasm collections generates an added value for genebanks, making this research a good investment. In this way, genebank curators can offer specific accessions with desired traits to plant geneticists and breeders, who can then select materials tailored to their objectives and needs. Photo: Pat Heslop-Harrison.

During the 20th Century national, regional and international gene banks established major collections for most crops to ensure the conservation of plant genetic resources. However, the use of this crop genetic endowment remains limited due to the lack of systematic research to provide a comprehensive framework for the efficient identification and introgression of beneficial variation for use in plant breeding. This needs to be achieved for both on-going priority traits and for novel added-value traits. There are now opportunities to develop new more efficient approaches for plant breeding because of the emergence of molecular genomic technologies and advances in computational systems. The power of molecular genomics will be fully realized when used in combination with classical quantitative genetics to integrate and comparatively analyze phenotypic, pedigree, and genotypic information for important traits. When we teach plant breeding we should therefore emphasize research and training in the use of crop diversity: conservation and characterization, plus the development of methods for increasing the pace and scope of impact from seed-embedded technologies. This training will require a broad range of partnerships, which will facilitate leveraging of new resources to harness emerging knowledge.

Research

The research agenda for hands-on training in plant breeding should include from crop biodiversity to bioinformatics with the main focus on analysis of genetic diversity of crops as well as development of strategies for conservation and utilization of genetic resources in plant breeding, with breeding informatics as a primary supportive tool. Over the last century assessment of variation in gene bank collections, and research into breeding and selection has led to a vast accumulation of both knowledge and genetic resources. For example, many breeding programs have collated extensive amounts of historical phenotypic and genealogical information on their breeding lines and some have conserved seed from these lines. However, rarely has this phenotypic data, derived from many years of multi-environment trials, been properly curated and integrated with genotype and site characterization data. The integration of interdisciplinary information resources and a comprehensive germplasm collection will facilitate the development of a new paradigm of knowledge-led plant breeding in which defined genomic regions will be the target for specific manipulation by plant breeding. Hence, all available data although sometimes patchy, can be used for retrospective modelling to form the basis of developing simulation tools to optimize the design of breeding and selection systems of ongoing breeding programs. The main pillars for teaching plant breeding course(s) should be:

Crop Biodiversity: Conservation, characterization and knowledge sharing

  • Developing evolutionary approaches for safe and dynamic conservation of the world’s crop heritage for future generations through further use in plant breeding
  • Exploring improved techniques for the conservation of plant genetic resources and the assessment of crop diversity
  • Understanding the rich genetic diversity of crops in the context of use in genetic enhancement, as the foundation for the development of dynamic core selectors
  • Modeling genetic diversity in agricultural crop species and their wild relatives to determine the extent of variation, clustering of germplasm for sampling, and identifying potential areas for further search

Genetic Variation: Targeted access and efficient utilization

  • Exploiting the untapped value of crop genetic resources through discovery of specific, strategically important traits required for current and future generations of target beneficiaries
  • Analyzing genetic variation (including association mapping for gene discovery and gene re-sequencing for allele mining) of target traits in respective genetic pools to facilitate their further “smart” use in plant breeding
  • Assessing innovative crop genetic enhancement methods that will lead to building “strategic germplasm blocks” through the utilization of unused “exotic” variation
  • Finding eco-friendly bio-techniques that facilitate the genetic manipulation of plants

Breeding Informatics: Building a functional link between biodiversity and plant breeding

  • Determining optimum use of molecular, genetic, phenotypic and genealogical data for “mining” germplasm collections
  • Turning data into knowledge and skills by visualizing results of whole crop genome description that will lead to a better understanding of gene × genotype × environment interactions, of great use in plant breeding
  • Simulating knowledge-driven breeding approaches for assisting genetic enhancement programs to choose the most appropriate parental genotypes, breeding systems and selection procedures
  • Participating in enhancing crop information systems and informatics platforms through a holistic framework in which to orientate the development of such tools, especially to ensure overall biological interpretations

Education … and Public Awareness

A group of people listening to a talk on crops.

Outreach and Education: Students should learn -through courses and research projects- to model genetic diversity in agricultural crop plants and their wild relatives, for both in situ and ex situ conservation, as well as for the sustainable use of genetic resources in crop improvement. They also need to acquire skills to make their case with the public and policy-makers to bring advances in Science for the benefit of humandkind. Photo: Pat Heslop-Harrison.

We increasingly require professionals with holistic interdisciplinary skills to help advance crop improvement. Integrated system-oriented thinking needs to be taught both at undergraduate and graduate levels. E-learning (through the use of web systems) should also become available as a supportive tool and reach students afar, especially through interactive modules allowing users to access knowledge and self-assess their performance. Likewise, we need awareness materials to educate and sensitize the general public and policy-makers to the needs for conservation and sustainable use of crop genetic resources through plant breeding. This may lead to mobilizing resources for large national, continental and international research partnerships with public and private sectors.

You can find out more about the research of the Department of Plant Breeding and Biotechnology at the Swedish University of Agricultural Sciences (in Swedish).

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Chips and the Washington Convention

Rainer Zenz/Wikimedia Commons

Rainer Zenz/Wikimedia Commons

CITES (the Convention on International Trade in Endangered Species of Wild Fauna and Flora – apparently, also known as the Washington Convention) is a treaty whose aim is to ensure that international trade in specimens of wild animals and plants does not threaten the survival of the species in the wild. Enacted in 1975, it offers varying degrees of protection to approx. 28 000 plant species.

The trouble is that the organisms ‘covered’ by CITES are – by definition – endangered and often in short supply. Consequently – sadly, economics applies in the biological arena as well as more human-sociological ones – those biologics are often in high demand, as ornaments, etc, in homes, offices, conference venues… So a CITES tag can actually be viewed as a price tag, the more highly endangered – and ‘cited’ – the organism, the more valuable. And there are ne’er do wells in the world for whom trade in such exotic taxa is a very lucrative business (allegedly).

Keeping a lid on this aspect of the black economy is difficult and policing the movements of the affected organisms is not necessarily the world’s number one priority. However, a relatively recent innovative procedure may just help to track such portable commodities as expensive botanics. Andrea Luvisi et al. expound on the merits of embedding microchips within ornamental shrubs (HortTechnology 20: 1037–1042, 2010). Developing the concept with roses they found that such shrubs should be safelytagged – internally – with a RFID (radiofrequency identification) microchip as early as the nursery phase, and without negative effects on plant appearance. We look forward to this being rolled out to more endangered plants in the near future. And let’s hope this news is timely enough to help the 75 vascular plants (along with 13 amphibians, 17 beetles, 81 crayfish, and 6 non-vascular plants…) whose endangered/protected status in the USA – under its own Endangered Species Act – is due to be reviewed  by the United States’ Fish and Wildlife Service (26 Sept. 2011 news release). Hmm, chips with everything? Now you’re talking!

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Towards a model for cut-rose

Towards a model for cut-rose

Towards a model for cut-rose

The production system of cut-rose (Rosa × hybrida) involves a complex combination of plant material, management practice and environment. Using XL programming, Buck-Sorlin et al. present a 3-D structural–functional model for the system that allows the creation of a wide range of initial structures thanks to simple interactive rules for pruning, cutting and bending. The model is able to reproduce PAR measurements taken at different canopy positions, times of the day and under different light regimes, and is able to predict local (per leaf) light absorption and photosynthesis.

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The scale of science and history (TIME 100)

TIME has recently published 100 greatest places in the world. The book is a collection of sites that, the editors argue, have had the biggest impact on world history. It’s excellent blog material because hardly anyone has read it (including me), any list will be personal and omit something someone feels is important and, following what the press releases say, at least one of the choices is intentionally trolling for controversy.

The Galapagos Islands, iconic in the history of Evolutionary Theory, but is this the place it was discovered?

The other reason for blogging about it is that it raises some interesting questions about the nature of science and history. I’m opening what will be three blog posts this week with a question about scale. What sort of scale is appropriate for examining the history of science?

The scale might seem obvious and the only real question is to argue whether it’s marked BC/AD or BCE/CE. That’s a scale of time or duration. To flip the question what is the smallest measurable unit of history? Is the action of leaping from a bath and shouting ‘Eureka!’ the shortest possible historical event? At the other end of the scale is the eradication of polio, which hasn’t finished yet, one long historical event?

The idea of scale was something that concerned the Annales school of historians. They divided history into three phases which, very briefly, were: Événements, events that happened in a defined moment. The Long Durée, long generational change that made one era different to another. Conjoncture, a third class of cyclical events that to some extent occupy the middle ground.

These kind of approach to history wasn’t popular with the English-speaking historians who disliked the Annales school’s belief that it was the Long Durée that was the history that mattered and that events were comparatively speaking, froth. The same approach has been welcomed by English-speaking archaeologists who find a lot of depth in this form of history, especially as archaeology is often rubbish at dealing with events or cycles and is best suited to studying long-term change. It also means they tend to skim things like conjonctures, hence my woolly definition above.

The reason I bring it up is that scale is interesting. The idea of a place mattering tends to suit events, but is world-changing science more a long-term trend. TIME chooses the Galapagos Islands as one of their places, because of the connection with Charles Darwin. The study of finches on the islands is one of the iconic moments of Natural Selection, but is it a place that changed the history of the world?

I don’t think it is. The Charles Darwin is the major figure associated with the development of evolutionary theory he wasn’t the only person to find it. He wasn’t even the first. The reason Darwin is so strongly associated with Natural Selection is illustrated by a reply he gave when Patrick Matthew, who said he had preceded Darwin in discovering Natural Selection and published his work in the book Naval Timber and Arboriculture.

I freely acknowledge that Mr. Matthew has anticipated by many years the explanation which I have offered of the origin of species, under the name of natural selection. I think that no one will feel surprised that neither I, nor apparently any other naturalist, has heard of Mr. Matthew’s views, considering how briefly they are given, and that they appeared in the Appendix to a work on Naval Timber and Arboriculture. I can do no more than offer my apologies to Mr. Matthew for my entire ignorance of his publication. (Gardeners’ Chronicle and Agricultural Gazette, 16. 21 April 1860. pp 362-363.)

What makes Darwin’s contribution stand out is that he told people about Natural Selection by writing a whole book about it rather than sticking the idea in an appendix. The book wasn’t simply “Here’s something I saw in the Galapagos Islands” it was a comprehensive exploration of the concept with plenty of examples drawn on. So if a place is connected with Natural Selection, shouldn’t it be Down House, where he wrote the book?

Possibly, but even writing the book is not enough. Lots of people have written books. On the Origin of Species was picked up, read and debated. Huxley was known as Darwin’s bulldog for the way he promoted Natural Selection, is the key place perhaps the Natural History Museum in Oxford where Huxley met Wilberforce? Is it the many places around the world after that found things made much more sense if you accepted Natural Selection?

So is place a sensible concept for a world-changing idea or are we using the wrong scale to look at scientific history? It could simply be a case of looking at the wrong thing. Pat has brought up a question in the office: Is the place more important than the person and, if so, where? That’s the next entry.

Photo: Lonesome George Pinta giant tortoise Santa Cruz by Putneymark licenced under a Creative Commons BY-SA licence.

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Simulating grazing of a 3-D sward canopy

Simulating grazing of a 3-D sward canopy

Simulating grazing of a 3-D sward canopy

The productivity and stability of grazed grassland rely on dynamic interactions between the sward and the animal. Combes et al. record 3-D canopy structures of swards of white clover (Trifolium repens) using an electromagnetic digitizer and adapted software, and synthesize virtual canopies in order to calculate bite mass of grazing animals and to determine effects on light interception efficiency (LIE) of the remaining sward. They find that bite mass and LIE values after grazing are more strongly affected by the initial structure of the sward than by bite form and placement.

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Modelling crown and wood characteristics of Pinus

Modelling crown and wood characteristics of Pinus

Modelling crown and wood characteristics of Pinus

Functional–structural tree models can be used not only for biomass and crown architecture modelling, but also for wood properties. Using L-system language, Fernández et al.  develop a model based on plant allometry and environmental signals so that a harmonic growth can be achieved, and by using monthly steps detailed three-dimensional information for crown and wood characteristics is obtained. The model is parameterized for Pinus radiata and validated against forestry inventory data with encouraging results, with the cyclical pattern and increase in growth rings being reasonably well modelled.

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On our Scoop It between November 15th and November 24th

These are links from our Scoop It page between November 15th and November 24th:

Happy Thanksgiving! Sweet Potato Gets Funding

While turkey is the star of the Thanksgiving plate, a humble side dish is getting its moment in the science spotlight. The Global Crop Diversity Trust and the International Potato Center in Peru have set aside $1 million for a renewable 5-year grant that aims to study and protect the crop. The grant is designed to help scientists study and maintain the tuber’s genetic diversity, as well as develop ways to make it more resistant to pests, disease, and weather changes.



Statistics: Odds Are, It’s Wrong – Science News

Science has long been married to mathematics. Generally it has been for the better. Especially since the days of Galileo and Newton, math has nurtured science. Rigorous mathematical methods have secured science’s fidelity to fact and conferred a timeless reliability to its findings.
During the past century, though, a mutant form of math has deflected science’s heart from the modes of calculation that had long served so faithfully. Science was seduced by statistics, the math rooted in the same principles that guarantee profits for Las Vegas casinos. Supposedly, the proper use of statistics makes relying on scientific results a safe bet. But in practice, widespread misuse of statistical methods makes science more like a crapshoot.



Lots of systems biology and control to think about in Google’s homage to SciFi writer Stanisław Lem

While my stream is filled with Google-Turkey doodles this morning, the actual current Google homepage (23 Nov www.google.com ) has a doodle very relevant to the systems biology thinking that I touched on in my cell and developmental biology course. It is based on animations of Science Fiction writer Stanisław Lem's work, but shows terrific examples of the different types of control mechanisms that can be used to achieve the same ends – a particular output based on an input and several switches for control. Can you think of examples with gene networks involving different control approaches? Are there any examples of redundancy in the doodle, and how robust are the controls to errors or perturbation? The waveform generator has many parallels in plant biology, with different examples of triangular waves, sine-waves, and switches/square waves, in various phases with the output. Think about feed-back and feed-forward for the man-in-the-cannon example too – how is that related to prediction of seasonal changes? What are biological inputs and outputs?



Louie Schwartzberg: The hidden beauty of pollination

http://www.ted.com Pollination: it's vital to life on Earth, but largely unseen by the human eye. Filmmaker Louie Schwartzberg shows us the intricate world. Pollination starts about 3:15



First night-flowering orchid discovered.

A night-flowering orchid, the first of its kind known to science, has been described by a team of botanists. Experts say the remarkable species is the only orchid known to consistently flower at night, but why it has adopted this behaviour remains a mystery.



» Leonardo’s Formula Explains Why Trees Don’t Splinter


Trees almost always grow so that the total thickness of their branches at a particular height is equal to the thickness of their trunks. Until now, no one has been able to explain why trees obey this rule, which Leonardo da Vinci first noticed.



Flirty Plants

If the sexual landscape of plants turns out to show abundant signs of fights and flirting, the tensions could easily play out in another phenomenon familiar from animals: battles of the sexes. Researchers are starting to look at conflicts for resources between male and female functions in the same plant. After the pollen bash in the bar, there could be some slaps on the face and door slamming in the parking lot.



Columbine flower shows off flowing tails

Researchers have discovered that the key to the different lengths of columbine spurs is the shape of the cells inside. Previously, it was thought that the different lengths were due to the number of cells. Columbines are a living example of evolutionary diversity – they come in over 70 species, each with flowers tailored to the length of their pollinators' tongues. The short, curled spurs of Aquilegia vulgaris attract bees, while the longer tails of the appropriately-named Aquilegia longissima appeal to hawkmoths.



AoB Blog – YouTube Channel

AoB now has a YouTube channel making it easier for you to access all the videos embedded on the blog :-)



Blog.1DegreeBio.org | 42 Reasons to Make Your Way to the Lab Each Morning

Why do you wake up in the morning and make your way to the lab after a reasonable amount of time, food consumption, and whatever else? What are your motives, driving forces, and points of no return? I have seen my share of weird rationales in my time, so I figured, why not share some of these with you here!

1. You love your project. It has been challenging, interesting, and refreshing.


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The good side to UV

David Shankbone/Wikimedia Commons.
David Shankbone/Wikimedia Commons.

Exposure to ultraviolet (UV) radiation is generally regarded to be deleterious to biological systems; however – like many potentially bad things – in small doses it may actually be beneficial. Well, that is what Jason Wargent and co-workers have found (Plant, Cell & Environment, 2011).

The UK-based research found that exposure of lettuce (Lactuca sativa) to UV-B in the early stages of growth led to increased photosynthetic activity and consequently higher yield(!). Or, in the more guarded parlance of the scientific paper, ‘Our findings suggest that earlier exposure to realistic levels of UV radiation leads to positive photosynthetic performance and other protective changes in leaf morphology, and when combined with enhanced photoprotection to high light and temperature as observed under controlled conditions, these early-stage effects driven by UV-B appear to enhance plant tolerance against generalized field transplantation stresses to a greater capacity, which can then lead to increased productivity in a longer-term field growth environment’.

Rather than repeat that, and in case you’ve missed the potential importance of this finding, the article’s abstract usefully concludes thus, ‘Our findings are discussed within the context of sustainability in agriculture and the paradigm shift in photobiology [slight emphasis added by me] which such beneficial responses to UV radiation could represent’(!!). And – because I know you’re wondering – I’m not aware that the famous leafy culinary vegetable’s green colouration was darkened by the treatment (by analogy to the tanning effect that occurs in human epidermides upon exposure to UV). So, your principal salad component should still be green (though why anybody eats the unsatisfying so-called foodstuff in the first place is beyond me).

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Partitioning model for fruit growth in cucumber

Partitioning model for fruit growth in cucumber

Partitioning model for fruit growth in cucumber

In cucumber (Cucumis sativus), imbalances in growth between individual fruits can be related to the partitioning of assimilates. Using L-Studio software, Wiechers et al.  develop a model combining architectural development, photosynthetic biochemistry and assimilate partitioning, with the latter including fruit growth. They find that simple partitioning models fail to simulate individual fruit growth realistically, but the introduction of thresholds for abortion and dominance related to source and sink strength, respectively, give results that are in line with measurements. Thus these factors need to be considered when simulating typical fruit growth traits.

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