Tag Archives: education

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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Planting the seeds

Dandelion Plant growth and development is a foundation concept in the science curriculum. Focus on plant characteristics and life cycles in early grades is particularly important because some evidence suggests that as children develop, their ability to notice plants, their assumptions about the importance of plants, and their interest in plants deteriorates. The conceptual understanding students develop about plants in the elementary grades therefore serves as a foundation for later science learning.

Work is needed to understand how elementary students can be supported to formulate scientific explanations, particularly about topics such as seed structure and function where students exhibit a variety of alternate conceptions. A new paper examines explanation-construction within the context of a long-term investigation about plants in three third-grade classrooms and asks the following research questions:

  1. How do third-grade students formulate written scientific explanations about seed structure and function?
  2. In what ways and why do third-grade teachers provide instructional support for students’ formulation of scientific explanations about seed structure and function?


Scientific Practices in Elementary Classrooms: Third-Grade Students’ Scientific Explanations for Seed Structure and Function. Science Education, 14 May 2014 doi: 10.1002/sce.21121
Abstract: Elementary science standards emphasize that students should develop conceptual understanding of the characteristics and life cycles of plants, yet few studies have focused on early learners’ reasoning about seed structure and function. The purpose of this study is twofold: to (a) examine third-grade students’ formulation of explanations about seed structure and function within the context of a commercially published science unit and (b) examine their teachers’ ideas about and instructional practices to support students’ formulation of scientific explanations. Data, collected around a long-term plant investigation, included classroom observations, teacher interviews, and students’ written artifacts. Study findings suggest a link between the teachers’ ideas about scientific explanations, their instructional scaffolding, and students’ written explanations. Teachers who emphasized a single “correct explanation” rarely supported their students’ explanation-construction, either through discourse or writing. However, one teacher emphasized the importance of each student generating his/her own explanation and more frequently supported students to do so in the classroom. The evidentiary basis of her students’ written explanations was found to be much stronger than those from students in the other two classrooms. Overall, these findings indicate that teachers’ conceptions about scientific explanations are crucial to their instructional practices, which may in turn impact students’ explanation-construction.


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Teaching kids about plants

Cattleya walkeriana When teaching about plants, science educators struggle with several problems in science or botany courses. Learning about plants is perceived to be less interesting than learning about animals, photographs of plants in textbooks are less numerous and less diverse than photographs of animals and attitudes toward plants are neutral rather than positive. Students also have serious misconceptions about the physiology of plants, and their abilities to name plants are limited. There is evidence that females have better knowledge about plants than males and that females appreciate plants more than males. A recent paper looks at the best way of teaching students about plants.

The study has several implications that should be taken into consideration in botany lessons. First, visual, colourful presentations of plants should include exposure of their fruits or seeds that promote information retention. In particular, contrasting colours of fruits may increase student’s attention, interest and consequently information retention about these plants. Second, talking about plants should contain survival-relevant information. This information includes plant edibility, the presence of toxic substances, medical importance of plants and incidences that can cause human death. For example, the hemlock (Conium maculatum) lacks any attractive seeds or other features potentially attractive to children, but the story of Socrates who was given a potent infusion of the hemlock and died can positively influence retention of information about this species. Finally, there was some evidence that the children involved in the research associated red colour with a fruit being edible, and black or green colours with toxic fruits, although this was not conclusive. Teachers should teach children that plants, similar to animals, possess aposematic, warning colours, and unknown fruits (with contrasting colour) should not be consumed.



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What a Plant Knows – MOOC Report

I’ll let you into a secret – I’m not really a plant scientist, I only masquarade as one on this blog. My day job involves science education and one of the main things I’m interested in is online learning, such as Massive Online Open Courses (MOOCs). This post first appeared on my personal/education blog, Science of the Invisible

What a Plant Knows What a Plant Knows comes as a refreshing change. This is down to the quality and enthusiasm of the teaching staff rather than any platform attribute.

Apart from a couple of statistics courses, the majority of the MOOCs I have taken were because I wanted to explore the platform and approach to learning being used rather than because of the subject matter. Coursera’s What a Plant Knows is different, because as the non-plant scientist Internet Consulting Editor of Annals of Botany, I feel that I really do want to learn more about plants.

Based on his book What a Plant Knows, Daniel Chamovitz fits into what I’ll call the Model B MOOC Professor – the big personality. In the grey world of MOOCs, this works well for me, although it would be very easy to tip over the edge and become irritating. As usual, there is a little too much talking head video, but clearly efforts have been made to include alternative formats. The assessment component is perfunctory, a few MCQs for each section. To their credit, teaching staff, including Daniel Chamovitz, are actively participating in the course discussions boards.

Week 1 was a good general introduction, although maybe slightly a little too “OH WOW, it’s a PLANT”. Week 2 on plant responses to light (“What A Plant Sees”) is right on the money – great stuff! Without any doubt this is the best Science MOOC I have seen yet.

Will this (very good) MOOC bring students flocking to the professional study of plant science? Not in any significant numbers – I can’t see us having to start a plant science degree to cope with student demand any time soon.


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What a Plant Knows – free online course

What a Plant Knows It’s a week until the free What a Plant Knows (and other things you didn’t know about plants) course begins. If you’re interested in an enjoyable online learning experience about plants, I’d recommend giving it a try.


About the Course:
For centuries we have collectively marveled at plant diversity and form – from Charles Darwin’s early fascination with stems and flowers to Seymour Krelborn’s distorted doting in Little Shop of Horrors. This course intends to present an intriguing and scientifically valid look at how plants themselves experience the world – from the colors they see to the sensations they feel. Highlighting the latest research in genetics and more, we will delve into the inner lives of plants and draw parallels with the human senses to reveal that we have much more in common with sunflowers and oak trees than we may realize. We’ll learn how plants know up from down, how they know when a neighbor has been infested by a group of hungry beetles, and whether they appreciate the music you’ve been playing for them or if they’re just deaf to the sounds around them. We’ll explore definitions of memory and consciousness as they relate to plants in asking whether we can say that plants might even be aware of their surroundings. This highly interdisciplinary course meshes historical studies with cutting edge modern research and will be relevant to all humans who seek their place in nature. This class has three main goals:

  1. To introduce you to basic plant biology by exploring plant senses (sight, smell, hearing, touch, taste, balance).
  2. To introduce you to biological research and the scientific method.
  3. To get the student to question life in general and what defines us as humans.

If it’s as good as his book with the same name, it should be a good course.

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Science and Plants for Schools – Biology practical demo – How do nettles sting?

This demo from Science and Plants for Schools demonstrates a quick and easy plant practical for biology labs. Using Universal Indicator paper, students investigate the pH of nettle stings. This can easily be built up into a broader investigation, or used as a quick practical to introduce the topics of plant defences, adaptations and specialised cells.

Download the full student sheet and teacher’s and technical notes free from the SAPS website:


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I feckin love the Dead Zoo

William Sealy Gosset I’ve just got back from a short holiday in Ireland which was divided into two parts – botanising on the West coast (of which more later), and a short stay in Dublin, one of my favourite places to visit. Because we had a few first timers with us on this trip, we had to pay the required pilgrimage to the home of Student’s t test, and while we were there, it would have been rude not to sample the local produce in the fabulous Gravity Bar – one of my favourite watering holes and thus familiar territory. But one of the places in Dublin I’ve never managed to visit before was the Natural History collection of the National Museum of Ireland, known to locals as the Dead Zoo (as you may be able to tell from the title, I picked up a smattering of the local patois on this trip).


The Dead Zoo I was blown away by the Dead Zoo
I’ve got a lot of respect for David Attenborough, but when you see a two year old come face to face with a polar bear for the first time you know the impact of that meeting is going to last the kid a lifetime. The best thing about the Dead Zoo is that there are no crappy, inoperative multimedia interpretations of anything – no greasy iPads, no frozen Windows displays, this is just pure zoology. It certainly took me back to museum visits in my childhood that have stayed with me and influenced my choices. I could have spent hours browsing the entomology displays alone – whole cabinets of springtails (my favourite) – but there were so many highlights, such as the glass sea anemones, and the “wall of bats”.


But where are all the plants?
I am aware that the National Botanic Gardens in Dublin are very good, and I hope to visit them on a subsequent trip, but I have a problem with a national museum which advertises itself as a Natural History collection when the only plant life on display is a few fossil ferns. Just what do they think all those dead animals are going to eat? Based primarily on Victorian and Edwardian collections, the Dead Zoo tells us something important about botany – that the public perception of plants as second rate science is not a new phenomenon. That was the only depressing thought to come out of my discovery of the Dead Zoo. It means we still have a mountain to climb.



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Focus on transfer cells

Image: Kelvin Song/Wikimedia Commons.

Image: Kelvin Song/Wikimedia Commons.

I love transfer cells. They are plant cells (which is great), but with a difference; they are ‘specialized parenchyma cells that have an increased surface area, due to infoldings of the plasma membrane. They facilitate the transport of sugars from a sugar source, mainly leaves, to a sugar sink, often developing fruits. They are found in nectaries of flowers and some carnivorous plants’. Those plasma membrane infoldings are the result of cell wall ingrowths and transfer cells (TCs) appear to have been present in angiosperms for over 50 million years.

The term ‘transfer cell’ was coined in recognition of proposed general functions in transferring solutes between interconnected protoplasts (symplast) and non-living spaces (apoplast) in or surrounding the plant. TCs are found in many widely dispersed plant types and their importance probably lies in their role in nutrient distribution, as they facilitate high rates of transport at sites that might otherwise present ‘bottlenecks’ for apo-/symplasmic solute exchange; e.g. crop yield in many species may ultimately depend as much upon proper functioning of internal TCs as it does on externally applied fertiliser(!). So, the more that is known about development, etc, of TCs the better for all of us. Well, good news then that Kiruba Chinnappa et al. have developed phloem parenchyma TCs in Arabidopsis as an experimental system to identify transcriptional regulators of wall ingrowth formation. Exploiting this system, they’ve so far identified ‘master switches’ that respond to various inductive signals to co-ordinate wall ingrowth deposition in TCs. Ultimately, the hope is that manipulation of this process may provide new opportunities for improving crop yield. I’m sure we can all wish them well in that noble endeavour.

[Ed. - And, if your appetite for TCs has now been whetted, these curious cells will feature in a future Research Topic in Frontiers of Plant Physiology to be edited by David McCurdy and Gregorio Hueros. But, if you can't wait until then, Felicity Andriunas et al.'s article "Intersection of transfer cells with phloem biology—broad evolutionary trends, function, and induction" is available now...]

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Algae found under teenager’s bed…

Image: Wikimedia Commons.

Image: Wikimedia Commons.

Shock, horror! But no surprises there you might think. After all, teenagers’ bedrooms are notorious ‘no-go’ areas for their parents – and others of a sensitive nature – and anything can develop (even new life forms!) in the insalubrious environment contained therein. But this is no ordinary tale of teenage grot. Rather, it is a carefully planned experiment carried out by 17-year old Sara Volz who was trying ‘to use guided evolution, so artificial selection, to isolate populations of algae cells with abnormally high oil content’.

Entitled ‘Optimizing algae biofuels: artificial selection to improve lipid synthesis’, her investigation used the herbicide sethoxydim to kill algae with low levels of acetyl-CoA carboxylase (ACCase), an enzyme crucial to lipid synthesis. Under this strong environmental pressure, the remaining artificially selected algae cells revealed significant increases in lipid accumulation. If those cells can be sustained, artificial selection could be used to increase microalgal oil yields and make algae biofuel viable. Well, her inquisitiveness within an imaginative laboratory setting(!) earned Sara (representing Cheyenne Mountain High School, Colorado Springs, USA) top prize in the Intel Science Talent Search (Intel STS), ‘the nation’s [i.e. USA’s] most prestigious science research competition for high school seniors’. The US$100 000 scholarship should go a long way to funding her studies at Massachusetts Institute of Technology (USA) where she is destined this autumn. As will what remains of the US$50 000 Davidsons Fellowship Scholarship Sara won in 2012 for a project entitled, ‘Enhancing algae biofuels: investigation of the environmental and enzymatic factors effecting algal lipid synthesis’. More usually employed as a post-emergence herbicide to control grass weeds in broad-leaved crops, sethoxydim apparently also has ‘indoor uses’. However, one imagines that the good people at Cornell didn’t envisage such an indoor use!

[Now, I don’t want to be picky, but to subject these claims to proper scrutiny, etc, we do need to know what the algae were. So, I did my own research, and eventually managed to find that Sara has ‘worked with several different strains – the ones I use currently are Chlorella vulgaris and Nannochloropsis salina…‘. But that information seems to predate the 2013 Intel STS project. So, we’re still uncertain of the species. Nevertheless, this young scientist is definitely one to watch! And not just because she was listed as one of the top 10 teen inventors in the USA by Popular Science magazine as far back as September 2011 – Ed.].


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Alice in the Wonderland of plants…

Alice-coverMilitary campaigns are sometimes intended to display ‘shock’ and ‘awe’ to overcome the adversary. Well – and rather less militaristically – Yiannis Manetas’ book, Alice in the Land of Plants: Biology of Plants and Their Importance for Planet Earth (hereafter referred to as Alice), is also intended to ‘surprise’ and ‘amaze’. And, like 21st century invasions of certain middle-eastern countries, but in its own quieter, more benign – though nevertheless subversive – way, Alice attempts to effect its own ‘regime change‘. The regime – “a system” – it is here attempting to change is the pernicious cult of zoochauvinism [or animal chauvinism, "the widespread tendency of biologists to consider it more important to study and teach about animals than about plants"; "a bias for animals and against plants"], which contributes to the condition known as ‘plant blindness’ ["the widespread lack of awareness of plants and neglect of plants both in biology education and in the general population"]. Ambitious? Certainly! Does it do its job? Well,…

The main text of Alice’s approx. 400 pages comprises a Preface, 10 Chapters, and an Epilogue. Whilst it is devoid of in-text illustrations (maybe to encourage us to imagine..?), it does have drawings of Alice at the front of each chapter which purport to summarise that chapter’s theme. [Is it just me, or does Alice look like a little like a hibiscus flower still in bud?] In the Preface Prof. Manetis confides that he considers writing this book to be part of a university professor’s duty, as part of a wider responsibility to transfer knowledge accumulated during the course of an academic career to the general public. Consequently, and as part of the mission to dispel plant blindness, Alice’s goal is to “share 30 years of plant study with readers so they can look at plants in a different – and friendly and entertaining – way” (p. viii).

Whilst I don’t intend to summarise every chapter in Alice, it is worth making mention specifically of some. For example, Chap. 1 “Introduction”, which includes such sections as “Plants are no less complex than animals: They are just different”, also makes the important point that plants’ significance is not limited to their resource use by humans, but also includes their role as ‘shapers’ and ‘moulders’ of Earth (which is probably the greatest – but largely unsung – and enduring importance of plants; pp. 2/3). Plant blindness is here considered (pp. 8-10), as are some interesting reflections on ‘popular science’ (pp. 10-12), and the practitioners thereof. Alice gets her first mention on p. 7, but without much build-up, the presumption being that all readers will already be familiar with Lewis Carroll’s 19th Century book ‘Alice’s adventures in Wonderland’ [AAIW] wherein a human – Alice – enters a very strange land which challenges many of her – i.e. our – preconceptions about everyday notions, objects, etc – and which are very much the same sorts of issues we are faced with as we try to understand the world of the plant. Chap. 2 “Basic Plant Organisation: How it Differs from that of Animals” provides important scene-setting for the tome, and hints at deeper consideration of phenomena mentioned later in the book. Other chapters are entitled “Why Trees are Almost Immortal and Other Related Issues”, “Short Evolutionary History of Plants”, “Sex in Nonmotile Organisms”, “The World through the Eyes of Plants”, “The Defence of a Stationary Organism”, “Symbioses Galore”, “Deviations from the Basic Biological Type”, and, finally, Chapter 10, probably the most contentious of all, “Are Plants Intelligent Organisms After All?” [Spoiler Alert No. 1: the answer is ... yes (with qualifications...)]. Bringing it all together, the Epilogue contains a 16 pp. tribute to Charles Darwin, in which Manetas makes the point that the overlooking of Darwin’s botanical work – and its relevance to his ideas on evolution – is yet another example of plant blindness. Surely, recognition of such flagrant disrespecting of that venerable Victorian should help push the cause for APB (Abolition of Plant-Blindness) forward!

Although references are not cited within the text – “to enhance the flow of the main text” (p. xi) – this omission does detract a little from any claims to scientific robusteness and pegagogic rigour that Alice might make. However, for further enlightenment, etc p. 361 lists 18 books (which includes many ‘standard‘ plant biology texts) as additional reading, and there are also approx. 5.5 pages of ‘reviews, opinions, and research papers’ (which includes >30 post-2005-dated items). The 3 pages of two-columned Index contain some surprises. For example there is no entry for chlorophyll, but there are 7 entries each for ‘stomata’, ‘respiration’, and ‘competition’; bizarrely, ‘affinity’ gets 6 entries(!), and even ‘asteroid’ and ‘aspirin’ merit 2 entries, each. Another surprise; the pages have very wide margins – c. half the width of the text. But, these expanses provide spaces for copious ‘marginal notes’ that “highlight essential points, guide the reader through the text, stimulate thought and memory, and serve as a verdict or final judgment on the issue at hand. Together they comprise a smaller book within the larger one that may be read separately” (Preface, p. xi)(!).

As a literary device AAIW has been used before in science writing, to capture that sense of awe and wonderment as unusual concepts and perception-challenging notions and ideas are dealt with. For example, AAIW is alluded to in Lamkanfi et al.‘s 2002 paper ‘Alice in caspase land. A phylogenetic analysis of caspases from worm to man’, and much more directly referenced in Ariah and Roberta Ben-naim’s 2011 book Alice’s Adventures in Water-land. Alice therefore seems an appropriate title for Manetas’ tome because it does aim to challenge – and change – (y)our perceptions about plants, and the entrenched view that perpetuates the myth that plants are boring and not that important; certainly not as important as animals. Plants are all around us, plant biology is therefore commonplace, yet at the same time it is incredible and fantastical, because much of it is beyond our own direct zoocentric understanding and experience of the world. Like Alice we are all exploring a marvellous land. But unlike Alice – Spoiler Alert No. 2 - we don’t wake up at the end of the journey to discover that it was all a dream. Fantastical though it is, this botanical Wonderland is very real and all around us; it is our waking world, and if we only opened our eyes to la vie en rose (en petunia, en thale cress, en potato, etc), we’d probably be much better off.

Generally, I found Alice to be well-written, thoughtful and thought-provoking, and very easy to read – largely because of its style (which reminded me a little of King’s ‘Reaching for the sun’). But, and despite Manetas’ intention that Alice is a book for the general public (p. xi), Alice is not necessarily one for the novice since it does include a lot of ‘textbook terms and concepts’, e.g. allelopathy, thermogenic respiration, horizontal gene transfer, PMSOs (polysubstrate monooxygenases (p. 253), which may be off-putting. However, all terms are explained and put in context. Still, Alice does contain some references that might not translate too well to a global audience (e.g. referring to Prof. Edmund Schulman’s realisation of how old bristle-cone pines can be upon counting their annual rings, “he must have felt the same as Professor Andronikos upon opening King Philip’s tomb”, p. 52 [presumably this is the Mediterranean countries' equivalent of Howard Carter and the opening of King Tutankhamun’s tomb – which may be more familiar to a UK/USA audience...]. But Alice is a book that is worth persevering with – you will learn a lot about plant biology, and especially about the interconnectedness of plant and planet (in which regard the section on ‘plants as environmental engineers’ – pp. 63-73 – and pp. 74-85’s ‘chemical history of the atmosphere’ are particularly interesting; both of which topics are not bad going for a chapter entitled “Why trees are almost immortal…”!).

Does Alice have competitors? Yes, sort of… Almost any standard botany/plant biology textbook – e.g. Mauseth’s ‘Botany’ or Evert and Eichhorn’s ‘Biology of plants’ – must be considered competitors for some of the factual content in Alice; but Alice doesn’t pretend to be a textbook, so such comparisons are probably misleading. Perhaps its major competitors are those texts that are also trying to deliver the ‘plants really are interesting and worth looking at…’ agenda, such as Beerling’s ‘Emerald Planet’, Hall’s ‘Plants as persons’, Koller’s ‘The restless plant’, and Chamovitz’s ‘What a plant knows’. But, each of those is different and none is a complete substitute for another. Alice is therefore pleasingly different and a great addition to the blossoming phytocentric literature.

To return to our rather tortured regime-change analogy, the Earth’s ancien régime is a plant-dominated one – plants after all were around long before us humans appeared on the scene, currently our world and ‘world-view’ is far too zoocentric/zoo-oriented. Arguably, we need to return to the former state of affairs. Not literally, but certainly in terms of giving plants the recognition and respect that they rightfully deserve, for all that we are now (and hope to become…). But, and important though it is, this tome’s goal will only be achieved if its message reaches those who are yet to be persuaded of the value and importance of plants; the fact that a botanist is here praising it is not enough! How we reach out to the ‘botanophobes’ is the real challenge. Nevertheless, Alice will help to remind the converted of the justness of our cause; we just have to keep spreading the word and convert the non-believers, and win over those hearts and minds. Vivat Alice! Vivat flora!


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