Wednesday, September 17, 2014

What does a grazed grassland look like?

Panorama of the trap pasture in Broken Kettle, IA

Over the past few days, I had a chance to visit some great prairies to do some work on bison.

The first was Broken Kettle in Iowa. Owned by The Nature Conservancy, it's the largest intact native tallgrass prairie in Iowa.

The second was Ordway Prairie in North Dakota. Also owned the The Nature Conservancy, it's unofficial claim to fame is having some of the largest bison in the US.

Each prairie is grazed, but they have different histories and current management.

While at each one, we talked about what grazed grasslands looked like and what to expect. For the managers, they need to try to fill conservation goals for bison, but also for birds that require habitats with different amounts of grass as well as promoting plant diversity.

A simple question of how many bison to stock becomes a complex analysis of examining the prairies.

So part of the what we talked about at each site was whether there was enough grazing, or too much.

One of the interesting features of the grazed areas at each site was how many forbs there were and at what density.

At Broken Kettle, a recently burned area looked like this:

When you look closely, the grasses are grazed down to golf course green height. Forbs are rare, but large. It reminded me of some grasslands in England and Scotland, except with Solidago instead of Cirsium.

The plant community at Broken Kettle in many spots is still recovering from aerial spraying of herbicides so one might not expect to have a broad distribution and diversity of forbs. 

In contrast, Ordway Prairie seems to be grazed less intensively (at least this year). It's hard to find places that were grazed hard. 

A lot of the grass seemed to be smooth brome (Bromus inermis). When you do find areas with forbs, it doesn't look the same as what was at Broken Kettle. The grasses aren't grazed down as hard and the forbs often seem crowded.

In all, there is still debate about what grazed grasslands look like. How much grass (and what species) should there be for sustainable grazing? How many forbs to expect?

It's a complex question, and I'm glossing over a lot.

Still, there's a lot of basic ecology left to work out about grasslands. A lot of people have different opinions, which are colored by their local site.

At the very least, I'd really like to see a coffee table book of just photos of grazed grasslands. Just seeing the diversity of grasslands out there would be an eye opener.**

Thursday, September 11, 2014

Short thought: funny line

"Amidst the whirlwind of molecular biological discovery it often seems overlooked that important metabolic processes are ultimately constrained not by biochemical pathways, but rather by the physics of plant structure."

Brodribb, T. J. 2009. Xylem hydraulic physiology: The functional backbone of terrestrial plant productivity. Plant Science 177:245-251.

Roots, water, and really tall grasses

Photobombing mom in front of some really tall grasses in Montpellier. 

Grasses are often synonymous with turf. Short plants that we can walk on.

But some grasses can grow to half the height of a redwood--50 m in height.

The physiological limits of tall height are often thought to reside in how a plant constructs its stems or leaves. Roots are important too, but mostly from an engineering perspective. They have to make sure the plant doesn't fall over. 

Turns out there is another role for roots that is unique to tall plants. They have push water up to the top.

Usually, when we think of roots and water, the soil-plant-water continuum concept of water movement has roots as semi-passive straws. Their job is to come in contact with water so it can be sucked up to leaves through the xylem.

But when water in the xylem is under tension it can embolize, producing an air gap in the rope of water that extends from the soil to the leaves. The consequence? Water ceases to flow.

Poke a hole in a straw and try to suck soda, if you want to test this out.

What's a plant to do once xylem embolizes? 

One approach is to grow new xylem and sacrifice the old. A lot of trees do this. 

Grasses can't do this, so they need to dissolve the embolism. Like squeezing a bottle of soda to get the bubbles to go back in, this takes pressure. 

How do some plants do this? Apparently, they close their stomata at night and let the roots start to pump up the pressure. 

Because of the gravitational forces at work, a short plant doesn't require much force to pressurize the entire shoot. A tall plant requires more.

Showing this had never been done before, but Cao et al (2012)** tested this with bamboos. 

**I'm apparently a few years slow in realizing how neat this paper is.

Turns out tall plants produced more root pressure at night than short plants. 

The work raises some interesting questions about the evolution of plants in general. 

Can short grasses produce as much pressure as tall plants, but just don't? It takes energy to produce pressure, but there might also be adaptations that coordinate root and shoot function. 

Also, for bamboos with stems, the point of growth is elevated off the ground. They don't grow from basal meristems. For cells to expand at the top of the plant, positive pressure is required. So, the root pressure should serve dual functions. 

Also, since we tend to think of xylem as under tension, we worry about air leaking into xylem. But, xylem can also be under positive pressure. Are there unique adaptations to making sure that water doesn't leak out of xylem at the wrong place? Hydraulic lift is thought to be passive based on the relative negative water potentials of plants and soils, but when roots are pressurizing the whole system, can't that force water out of some roots? 

None of this information is going to help create grasses that don't have to be mowed as often, but it sheds serious light into the evolution of height in plants (even grasses).

Cao, K. F., S. J. Yang, Y. J. Zhang, and T. J. Brodribb. 2012. The maximum height of grasses is determined by roots. Ecology Letters 15:666-672.

Wednesday, September 10, 2014

From The Haiku of Writing a Paper: Introduction

Some people have said that I can write papers quickly. I'm not sure if that's true or not, but I have learned to write them faster than before. And part of that is having a standard structure to guide the writing process.

A long time back, I tried to crystallize what I had learned about putting together scientific papers. Mostly from making a lot of mistakes. I did it mostly just to get all the different ideas organized for myself.

The general approach was to reduce the structure of the paper down to a skeleton outline. Not quite a haiku, but close.

Apparently, the full document has been passed around a bit--I'm always surprised when people tell me they were using it.

As an example, introductions can be tricky to write. In most of my papers I try to follow the 3+1 model. With this model, you funnel from big ideas to specific points to be tested.
First Paragraph: Big question. This is the general broad reference to your work. For example, it might be that atmospheric CO2 concentrations are rising, or nitrogen is an important driver of ecosystem dynamics. 

Second Paragraph: Proximal question. Within the broader framework, the proximal question should be stated that you are directly addressing. For example, although atmospheric CO2 concentrations are rising, the controls over soil C storage are poorly known. Or although nitrogen controls ecosystem dynamic, there are important questions regarding the role of denitrification in controlling N availability. Note that a proximal question can often be framed as the big question—it’s all a matter of perspective and how you want to tell the story.

Third Paragraph:  Scope of research with hypotheses. In order to better understand the role of soil C storage in responses of ecosystem to elevated CO2, we tested whether elevated CO2 increased the C stored in the soil within soil aggregates.

The "Plus One" Paragraph: Competing hypotheses. The best introductions and research designs test between competing hypotheses. Often when there is a single hypothesis that is rejected, the authors can derive alternative explanations that don’t require the theory to be rejected. Therefore, might as well start with competing hypotheses since there are always competing hypotheses. Framing the hypothesis in the null form is not necessary when using competing hypotheses. For example, in testing the role of N in decomposition, an experiment could test whether stoichiometry predicted responses of decomposition to greater N availability. Or we can test between stoichiometry or N mining in predicting the responses of decomposition to greater N availability. No on experiment is generally able to reject a theory, so you can test between two theories and whether data supports one theory or another.

Note, I call the last paragraph the +1 paragraph, because it isn't always there in a paper--it depends on design.

Still, using this model, you should be able to write your introduction in 3 or 4 sentences. Once you have that you can expand each sentence to a paragraph. These can be expanded out more to maybe 2 paragraphs, but if you deviate too far from this, the introduction is likely running long and will be confusing to readers.

There are tricks to writing other sections efficiently and a lot of details to look after as you get through the sections.Still, once you settle in on your framework for papers, it makes writing the paper a lot more fun, since you can concentrate on the message rather than the structure.

Tuesday, September 9, 2014

Modeling water flow in soils and plants

Reading more about modeling water uptake by plants.

Like this figure from Lobet et al. 2014, so I though' I'd add it here.

Sunday, September 7, 2014

Book Review: The Bee: A Natural History

Honey bees.

Bumble bees.

Sweat bees.

Queens, drones, pollination, waggle dances.

I'm not sure, but that list might have been about 90% of what I knew about bees.

Add that I'm allergic to bee stings** and we're up to 95%.

**When I get stung, the affected area tends to swell up. I once got stung on the hand while on the south shore of Lake Itasca helping Kendra with vegetation surveys. My hand swelled up pretty severely, but luckily it froze into a claw shape and I could paddle back to our cabin on the north shore. Another time I got stung in the lip while in South Africa after taking a sip of a soda. Apparently a bee had climbed into the can while I wasn't looking. I remember wearing a bandana for 2 days because my face looked so hideous.

After reading Noah Wilson-Rich's The Bee (Princeton University Press), I think my previous knowledge set on bees is much larger.

First, the book is rich in pictorials. Almost to the level of a DK Eyewitness book, but with more text and more information.

The visual jewel of the book is the section "A Directory of Bees". The section has half page enlargements of  forty of so bees from around the world. Solitary bees such as the 2mm Perdita minima to the 40 mm Wallace's Giant Bee. Each bee has a description and a section on behavior and its life cycle.

Other sections include the evolution of bees, their anatomy, their societies, and the history of bees and people.

Reading the book reminds me of the immense effort it takes to understand biodiversity.

Not biodiversity abstracted to an index, but each defining detail of every organism. Organisms have a long evolutionary history and a complex ecology. Multiply that by the 20,000 species of bees that exist and it's a life's work to just to start to understand it.

For bees, it is their evolution from wasps a hundred million years ago. The immense floral radiation that they initiated. The eusociality of some bees is what sets them apart, but so many of them are solitary, which is fascinating in its own right. And how they produce honey, wax, royal jelly, propolis (!), and venom from a few food sources is equally fascinating. And the things that attack bees: Foulbrood, Chalbrood, Nosema, deformed wing viruses, mites, beetles, moths...

I really appreciated this book.

By the time I was done reading the book, I felt like I had superficial, but robust knowledge of bees.

And that was more than when I started.

Well done to the main author and the other authors that contributed.

May more natural historians be inspired to write similar volumes.

Wednesday, September 3, 2014

On thinking long thoughts

"It's not enough to fail. You have to come to feel your failure, to live through it, to turn it over in your hand, like a stone with strange markings."--James Fenton

The other night, this blog experienced its 100,000th page view.

I'm not sure how reliable that number is, but this isn't a bad time to step back and take a few moments to reflect just a little bit.

I started this blog in January of 2009. My book, Resource Strategies of Wild Plants, was about to be released and I thought it would be good to have a space to explore ideas.

In time, the blog is more of a scratch pad for me. It forces me to slow down a bit and coalesce my thoughts just a little bit.

Since the start, I've put together over 250 posts in that time. Each one a different thought. That's not that many.

How long is a thought though?

Thoughts seem like they should be short.

140 characters is a standard these days.

An abstract to a paper might be considered an extended thought. Those are about 250 words.

A blog post might be a bit shorter or longer. Sometimes 50. Sometimes 500.

A typical NYT editorial is about 750 words.

The body of a scientific paper can be 1500 words in a condensed journal. 15,000 words in a longer review.

A book? Mine was about 100,000 words.

All of these are thoughts to one degree or another. But they differ in the time it takes to assemble and connect the ideas contained within them.

Short thoughts are quick to think. It takes a few seconds to have a short thought.

Long thoughts take longer.

When I was writing the book, I kept track of word count each day. It takes a long time to get to 100,000 words.

But it takes more than just a large accumulation of time.

Stitching short thoughts into long thoughts is hard.

Time has to be free of distractions. You have to find quiet time to begin to take short thoughts and stitch them together into something longer.

It also requires the dialectic. Sometimes internal. Sometimes external. Argument is essential. It pulls threads into cloth. Turn ideas over. Examine them from all directions. Poke and prod as you go. Find the weak points. Practice connecting them to other ideas.

To produce long thoughts you also have to take in thoughts slowly. Read books. Tweets, blogs, emails, abstracts, even papers all have their place. But books are the longest thoughts we have. Reading a book will slow you down.

Taking a long walk with a person and conversing on the same topic for a mile will do that, too.

You might guess that I'm not convinced that shortening the thought process is uniformly beneficial. Short thoughts can be absorbed quickly, but they do not necessarily constitute knowledge.

Science can progress rapidly, but many of us are working on the same questions we were working on 20 years ago. Science moves slowly, too.

How do you reliably push things ahead?

Think long thoughts.

Tuesday, September 2, 2014

Home microbiomes

Shared phylotypes heatmap for individual surfaces after consolidation of samples taken from the same surface type across temporal sampling series and homes

Noah has had me reading papers on microbial communities lately. 

The latest paper in Science by Lax et al. has some interesting aspects. 

The authors had 7 families swap standardized surfaces over 6 weeks. A few families even moved.

Microbial communities were tracked over time. 

Part of the interesting things they found was akin to forensics. People left microbial fingerprints on household surfaces. When a family moved into a new home, the fingerprint was rapidly established.

The best match between body parts and surfaces? 

Feet and kitchen floors. 

Hands and door knobs or light switches? Not so much, but still pretty good.

Noses? Didn't leave a microbial noseprint on anything.

I guess no noses pressed up against the window glass. Or no microbes being "picked" up by hands in those families.

Lax, S., D. P. Smith, J. Hampton-Marcell, S. M. Owens, K. M. Handley, N. M. Scott, S. M. Gibbons, P. Larsen, B. D. Shogan, S. Weiss, et al. 2014. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science 345:1048-1052.