​In a research world more and more obsessed with publish or perish, submitting research manuscripts can be a daunting hill to climb as a new researcher. That hill turns into a mountain when those results go against an existing paradigm.
 
This second blog is also inspired by the Rooting 2017 meeting in Umea in May (see the last blog here) and some amazing conversations I had with several PhD students and postdocs who have convincing results that go against different ideas in the root world.  Despite discouragement from supervisors who thought the experiments wouldn't work, these researchers often did experiments anyway to produce truly interesting results!
 
This brings me to my first point: CONGRATULATIONS! YOU ARE NOW A BONIFIED RESEARCHER!
This really excites me - seeing the next cohort of research leaders thinking, testing and following their instinct and logic to do amazing science.
 
What worries me, however, is the consistent feeling of dread amongst these fantastic people regarding publishing these potentially controversial results and their impression that they won't be believed because they 'are nobody'. 
 
My next point then: You are not nobody.  Those big names were unknowns once!
And they typically built their careers on making some big findings that went against those before them. This is how science works (often in small steps, sometimes in paradigm shifts!). And often it's not that they were wrong (although sometimes…) but rather understanding has progressed to better tease out the science underneath, or new techniques have become available that weren't possible before, shedding light on the topic.
 
Ok so that's all good and well and I'm sure none of that makes any of you amazing new scientists feel any better about the challenge ahead of you! So I contacted a range of editors from several journals (from ecology and plant science fields) to get their take on how to publish something that goes against existing ideas.
 
One quote that should immediately cheer you:
 "‘Something not in line with existing understanding’: isn’t the simple answer that this is what we’re all looking for – scientists and journals?" 

Here's another:
"I think that giving a field a new direction with results that contradict the current model is as exciting as new discoveries. Science is not written in stone, it is constantly evolving. A published peer-reviewed scientific paper is not a definite and absolute truth, it is more like a temporary working hypothesis waiting to be confirmed by other labs, or to be used to go even further."
 
The following four points were made by each editor and I've paraphrased to incorporate all of their points.

1. It often takes time to make a paradigm shift - so don't give up!
2. Journals are not faceless computer programs (which is how I felt until very recently) but they are in fact run by actual real live people - so you can talk to them about your manuscript. And you can do this at any stage. They will tell you what they are after. "You might get in touch with one of the editors or the journal office and see whether there are options for getting your ideas out there – many journals do have outlets for more speculative ideas."
3. You need to build the case for your results thoroughly. Starting from the methods you used and demonstrate the results from different angles. "the only advice I have is the one from Carl Sagan: “Extraordinary claims need extraordinary evidence”. We don’t have a problem with claims that are not in line with what is currently known, but they will need very robust data (like any claim of course)."
4. Different journals have different ways of sending out for review. For example some offer double blind reviewing (and others name the reviewers) instead of only reviewers being anonymous. Some also have editors who are full time employees of the journal (with no dog in the fight) while others are time-strapped researchers at universities who may have been involved in some of the original research (who may still be just as excited by your findings!).

 
 
So go for it! I'm looking forward to seeing these bright sparks light up the hidden half!
 I'm going to end with a quote which sums up things I've said in previous blogs:
 
"And if at first it doesn’t progress, use the advice provided and don’t give up.”


Thanks to the editors who took the time to comment and provide these inspirational quotes!

Happy Monday morning to you all! (yes I think reading or writing blogs is a great way to procrastinate at the beginning of the week too!). 
I've just returned from the Rooting2017 conference in Umea, Sweden and this blog and at least one other are inspired by that meeting (so watch this space for the next one too). 
Today's blog is inspired by some comments on the first day that were in my (Australian/Britified) mind unnecessarily narky. What follows is more or less what I said in my seminar on the morning of day two so if you were there no need to read any further! 
The first thing I will say is that I understand full well how protective we become of our research niche. This is driven by the nature of the research world we are part of with competition for jobs, and grants and the push for higher impact papers, and promotions (all of these being interlinked). And when we face rejection after rejection it's easy to become defensive. 
However when someone has prepared a conference talk of their beloved system and opened their bubble to share it with a room full of critical, (often cynical) scientists - this is the most nerve wracking thing (at all levels - professors I've spoken with tell me they still get nervous)! The least we, as the privileged audience, can do is ask science based questions rather than making unhelpful comments on the relevance of their experimental system in a real world context. 
And this is where the point of my blog begins. 
Excluding some ecological research here and talking mainly about experimental biology (and probably experimental science in general) - we all work with experimental systems. We try to control as many variables as possible in order to understand one small part of an otherwise very complex set of systems. Whether we are using model species, or using some obscure interesting plant within a controlled growth chamber (or mathematical models for that matter) - we are all using models to simplify the complexity of the natural world. In a statistics text book I was reading the week before the conference (yes I'm that geeky and no I don't understand statistics!) the author (Crawley, Imperial College London) makes the comment that all models are wrong. Now he was referring to statistical models but they are built around our experimental models so by extension we are all wrong. You, me, everyone. 

But that's ok!
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We are all simplifying nature and there is no perfect way to do that (which is also what Crawley was saying).
My point is (and that of the review paper in 2016 that I was also discussing in my talk) that all experimental systems have limitations as well as advantages. This means that every piece of well thought out research is of value to the greater knowledge bank. The only thing that limits the value of any experiment is how well we communicate the details of the experimental system and why we chose to use it. This of course will also then affect how easily manuscript reviewers understand the manuscript and how many times our work is cited (all important for citation indices and promotions etc).

So be clear about the details of the system you choose and remember that no matter who you are or what system you work with your research is important and valid! 

I'll end with a quote from an interesting chapter in Sustainable agroecosystem management (reference below):

"In its purest form, reductionism searches for mechanisms among the constituents of a system and holds that understanding the constituents is sufficient to understanding the system. Reductionism helps us make sense of the world; it is intuitive and generally it works. The beauty of reductionism is its simplicity and the relative ease of experimentally demonstrating cause and effect within system components. By controlling the variables, interpreting experimental results is relatively straightforward. On the other hand, the weakness of reductionism derives from its inability to predict system behavior that arises from interactions among its components."


Phelan PL (2009) Ecology-based agriculture and the next Green Revolution. Is modern agriculture exempt from the laws of ecology? In: Bohlen P, House G (eds) Sustainable agroecosystem management. Boca Raton, pp. 98–128

Also mentioned in the interesting review: Paungfoo-Lonhienne C., Visser J., Lonhienne T.G.A. & Schmidt S. (2012) Past, present and future of organic nutrients. Plant and Soil, 359, 1-18.

The review I was also discussing in my seminar: (shameless self advertising)
Steffens B. & Rasmussen A. (2016) The Physiology of Adventitious Roots. Plant Physiology, 170, 603-617.

I love science fiction and I especially love Dr Who so when I find a chance to connect that love with my other love - plant science - I just have to blog about it!
 
Last night's episode was filled with planty references but I can't go past the scene where a swarm of tiny robots are pollinating a wheat field (let's ignore the fact that wheat is wind pollinated for a minute) on a foreign planet. 

Fiction I here you say!
Well… maybe not.
 
To explore this out-of-this-world concept we first need to know what is pollination?  According to my first year biology text book (Campbell, Reece and Mitchell) pollination is 'the placing of pollen onto the stigma of a carpel'. But what does that mean???  Let's use a picture to help. In plants, the male bits are the stamens with their anthers (which present the pollen), while the female bits are the carpels which include the stigma (sticky bit ready for pollen), the style (which the pollen tube grows down) and the ovary. Today's ramble is only about pollination but the rest of fertilisation (including pollen tube growth) is equally fascinating!
 














(picture from:
http://www.all-my-favourite-flower-names.com/parts-of-a-flower.html)

Pollination can occur in many different ways including wind (as hay fever sufferers well know), animals and insects - bees being the most well-known and perhaps the most important economically. 

At this point, dear readers I highly recommend taking 7 minutes to watch this TED talk which has some nice pictures of pollination in action!
 
Click Here
 
Amazing right?!

As many of you will be aware the bee populations have been declining due to a range of causes (some of which we still don't understand - and perhaps partly due to them returning to their home planet Melissa Majora as the Doctor told us in 2008!).
 
At this point I want to say that our first priority should be to protect the bees (and all pollinators) but let's imagine for a moment we are travellers to a far away planet with no pollinators - could robots be the answer?
 
Earlier this year a paper in Chem http://doi.org/10.1016/j.chempr.2017.01.008 made waves with their artificial pollinators. Many of you may have seen some of the headlines as you scrolled through Twitter but I wonder how many of you stopped and read the original article? I didn't - until today. So here is the roundup.
 
The authors had a series of problems to overcome. The first was to find an adhesive that can pick up pollen efficiently but would also let go of the grains when in contact with the stigma (sticky female bit - see pic above), was non-toxic and water resistant. Their solution was an ionic liquid gel.

The second problem was to determine if their gel was suitable for biological applications and non-toxic. They used a lab test on cells which were treated with the gel and found that small volumes had no significant effect on the number of living cells meaning that it was safe to use on biological systems.

Ecologically, introducing little robots into the food chain could be a problem but the team could see their gel also being used for camouflage - reducing predation. Into their gel they mixed four different organic compounds which can change colour depending on the light and then painted flies and ants with the gel. As you can see (and I think this is as cool as the robotics part of this story) the gel changed colour with more UV light. 

The insects painted with the gel were able to move and interact within the flower, collecting pollen more effectively than non-painted insects.
So they had a gel that worked on insects. 

The next challenge was to create a robotic insect. In insects the pollen gets transferred from the anther to hair on the insect's body. So the group coated different fibres with their gel and tested how well pollen would stick. The fibres came from everyday products like paint brushes and make-up brushes. They found the animal hair brushes (horse hair paint brushes) and nylon (from make-up brushes) worked well when coated with the gel but they found carbon fibres were unsuccessful because they were too big.  They decided to stick with horse hair for future experiments because of biodegradability in the natural environment.

The story is emerging: they have their sticky-gel, which is safe for use in the environment and now they have their fibres for mimicking pollinator hair - the only thing left is the flying machines!
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They used commercially available small UAVs (Unmanned aerial vehicle) which was just 42 mm long by 42 mm wide and 22 mm high. They stuck the gel-coated fibres on the back of the UAV with double sided tape (and checked that launch was unaffected by the fibres) and then used radiocontrols to fly the robotic bee to the Lilly flower, collect pollen and deposit it on the stigma - see the movie in the file below). They checked viability of pollination using microscopy and found successful pollen tube formation. 

So although these UAVs may be slightly clumsy looking - they work. The next step is to make them smaller, fly more precisely and fly alone and then off-world robotic pollination might not be such a stretch of the imagination!


References: 
The article on robotic pollination can be found here: 
http://doi.org/10.1016/j.chempr.2017.01.008 and the colour-changing fly picture and the movie file come from this source. 

The textbook I used for pollination definition is: Campbell, Reece and Mitchell (1999) Biology (Fifth Edition) published by Benjamin/Cummings ISBN: 0-8053-6566-4.

The TED talk on pollination comes from: 
​https://www.ted.com/talks/louie_schwartzberg_the_hidden_beauty_of_pollination#t-437315
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The flower picture came from this random website (it was the prettiest image!): http://www.all-my-favourite-flower-names.com/parts-of-a-flower.html

Link below isn't working: but this one is :)   
http://www.nottingham.ac.uk/biosciences/events/holdenbotanylecture.aspx

Come along on the 2nd May 
Feel free to get in touch if you have more questions.

On the 2nd of May I'm honoured to be hosting Dr Sandra Knapp from the Natural History Museum (http://www.nhm.ac.uk/) for the Holden Botany Lecture. 

The Holden Botany Lecture is a public seminar held once every two years and named after Prof. Henry Smith Holden who, in 1932, was our first Professor of Botany at the University of Nottingham. The first of these lectures was held in 1975 with the intention that the ‘lecture be given by a distinguished botanist, biologist, or an industrial or horticultural specialist, and would emphasise the importance of basic botanical and biological research work’.

With this in mind Dr Sandra Knapp's impressive career working with the taxonomy of Solanum, Capsicum, and Lycianthes with the Natural History Museum clearly makes her a natural choice for this year’s seminar. 

The seminar is open to all so if you find yourself in the East Midlands do come along! More details for the event can be found at:  www.nottingham.ac.uk/go/holdenbotanylecture or you can email me with any questions. 
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See you on the 2nd May!

It's been a while since I posted so prepare yourselves for a longer than usual blog!  I was going to separate some of these topics into separate entries but honestly I can't be bothered so you'll just have to read (or skim) the whole update!

First to Students (and no they aren't related to stress!) - I've had the great pleasure of having Jordan in my lab for a DTP rotation for the last 7 weeks. She has been learning about maize growth and the soil-plant-air continuum. Some of the techniques she has learnt include 15N uptake (which is what we are doing in the images below), shoot and root biomass measurements, CT imaging of roots, leaf pigment stuff (which is sort of my loose connection to stress!) and microdialysis sampling of soil nutrients.  The last 7 weeks have been a lot of fun and I'm sure whatever project Jordan chooses she will go on to great things! 

Now to Stress - not mine - and actually not really stress but rather plant pigments which can indicate stress!  Those of you following me on Twitter will see that I recently obtained a Dualex meter. This measures chlorophyll, polyphenols (flavonoids) and a ratio between the two (for more detail see Force-A page: http://www.force-a.com/en/capteurs-scientifiques/dualex-scientific/
​and download the brochure).

The reason I am so blatantly advertising the for Force-A is because of the support they showed me during the nightmare of having the device delivered. Firstly - to order a piece of equipment like this is a serious decision when there is a limited budget so I put a lot of thought into weighing up my options. Having decided to order one Force-A were fantastic with getting it packaged up and sent. However a certain delivery company who can remain unnamed (but whose initials are U. .P...S) seem to have lost the delivery but refuse to accept their error (details can remain out of this due to further investigations - however it seems I'm not the only person to have problems with this company!). The device should have arrived the first week of November 2016 but has still not been located. Force-A are not at fault so have no obligation to do anything further, however despite this they stepped up and provided a replacement device (via a different delivery company) and the device arrived 2 working days later! It has been rare for me to experience such charity and support and I truly appreciate it - in particular as a new academic with a tight budget. 
Since the Dualex arrived we (I mean Jordan!) has had a play and measured a bunch of random plants around the place....data below....definition of the ratios are given in the picture above. In future the dualex will allow us to do continuous measurements of leaf status. At the end of experiments we'll make a final measurement, harvest that tissue and use colorimetric methods to measure whole tissue pigment concentrations. Fun times to come!  
​So thanks again Force-A  :) 

That brings me to stuff! 

I watched this fabulous TED talk (link below) recently on mentoring and how to get the most out of your team.  I personally have had more bad than good experiences with supervisors and I'm always on the lookout for good advice. This one however hit home hard regarding the chicken-run of academia and the encouragement of superchickens rather than ensuring all the rest of us chickens are happy, healthy and as a collective more productive. It's a fantastic talk (like most TED talks) and I think if this way of thinking and behaving could be incorporated more into institutions it will not only improve overall productivity but also make a community of much happier chickens! 
http://www.ted.com/talks/margaret_heffernan_why_it_s_time_to_forget_the_pecking_order_at_work 

Finally - AR-Lab is moving....Again! This time by choice - just across the Sutton Bonington Campus to Gateway building. It's been two days (and most of today I was teaching) but already I feel very welcome among my colleagues and have been able to pop in and ask questions or have a chat with people as I've bumped into them when previously I would have had to walk across campus to see if they were in! So thanks to you all for making me welcome! My email contacts stay the same, phone number will change (see my contacts page). 

If you've read all the way to the end then I thank you for thinking this was more interesting than spending your time on something else! :) 

Congratulations to Olivia Cousins (an Adelaide-Nottingham joint PhD candidate and one of our team!) who won the student poster prize at the 2016 New Zealand Society of Soil Science and Soil Science Australia conference held in Queenstown, New Zealand 12-16th December this year. A full version of the poster can be found at: soilecology.org/conference-posters 
​
Well done Olivia! 

I thought it was about time for an update from the AR_Lab! 
Aside from full recruitment mode there have also been some fun stuff going on wtih the plants. The new rhizoboxes are in the glasshouse and the plants are very happily growing. I'm still amazed (even as a root physiologist) by how extensive the root system can be for a comparatively small shoot - and these are all growing with sufficient nutrient availability. 
While we're talking about plants in action the second edition of this very useful text book is now online and freely available for all to use. You can find it at ​http://plantsinaction.science.uq.edu.au/ 

These boxes will never look this clean ever again! This was the evening they were delivered. :)

This is my advertising shot - beautiful blue skies at Sutton Bonington that day :)  Boxes filled with potting mix and ready to go! (by the way blue skies are not actually unusual here!)

Plants in action! Measuring nutrient uptake from root types without disturbing the plants. Check out how long the roots are compared to the shoots! After half an hour the treated roots were cut off and the windows were replaced, retilted and recovered with opaque plastic as if nothing had ever happened!
​So many great experiments to do! :) 

I was just reflecting on my day today and I think there's a good analogy that can be instructional regarding what plant physiology means. 

The analogy comes from my medical check-up at the hospital today (hence having the time for two blog posts! - all good for another year by the way ;) ).  At the hospital I'm always greeted by "Hi, I'm Joe Blogs and I'll be your physiologist today".  That physiologist then connects an ECG, and logs in to my pacemaker and checks the readings from the two are comparable and then they download all the data from the time in between which has been recorded by the pacemaker and check certain features of the functioning of my heart. They then manipulate the heart rate using the pacemaker to see how everything responds. 

This is exactly what plant physiologists try to do. Instead of a person as a patient, it's a plant, instead of an ECG it might be a LiCOR or a pressure bomb and instead of a pacemaker it might be a heat pulse velocity kit (which has various other names), or a dendrometer, and the data is collected by data loggers (just like the pacemaker) or by us (just like the doctor).

There are lots of other techniques that we use - all of which measure processes. observing the shape or colour is of course of interest - particularly when we can do this many times- because they tell us something about the outcome of the processes.  
Note the use of the word 'outcome'. Without knowing something about likely processes involved we can't use a single image or set of images to understand physiology.

Having said that, once we know the processes that lead to a visual outcome we can very effectively use images of that outcome as an indicator of the processes (by inference so it's important to check from time to time). - I'm of course referring to phenotyping. 

The other thing I'm going to say is that of course just like it's possible there is a genetic basis for my heart defect (which we have no evidence for currently) many plant physiology process defects (or changes) are related to genetic effects but just because changing one set of genes leads to a set phenotype - there are many possible processes that may have changed to come up with the resulting image and there are many different process-paths that could have been taken and without studying the processes, we can not know which processes changed or responded. 

Again the genetic tools available now are opening physiology doors that were not possible 20 years ago - these are essential tools developed by fantastic molecular biologists and geneticists (and bioinformaticians).

So what is my point in all this rambling?  

My point is that with the previous revolution in genetics and molecular biology and the current revolution in phenotyping technologies, the physiology skills and knowledge have become untrendy (is that a word?) and so are dwindling - but they are essential!  In the UK this has been acknowledged (at least in writing) by the BBSRC - so I'm not making this up - at least not entirely (it is of course a biased perspective of a physiologist!). 

So why is physiology untrendy? I have no idea! This is an exciting time for plant physiologists! We now have the ability to adapt the tools and technologies that have been used in medical physiology for plants (those pesky cell walls tend to make adapting essential but modern materials are making this possible). 

Anyway I think the first step is to remind the world what physiology is! So think about the pacemaker and the physiologists who monitor all the heart processes- and then replace the patient with a plant. 

Small disclaimer:  If any human physiologists read this - I know they are doing a lot more when I go in for tests than what I listed here, so I'm sorry for not doing that justice!

There's also a fabulous picture of my boxes with Spongebob trying to get out somewhere on twitter! :) - you'll have to look it up to see the reason! 

So that's my update.  So many other things going on too - never a dull moment!  

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