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.

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.

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.

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.

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.

Modeling competition for water: calling the race

Sensitivity of water uptake to changes in parameters for crops grown with weeds or weed-free. Parameters in the lower right are a lot more important when competing against weeds than when weed-free.

When competition is a race from the start line--like with crops--the best strategy is to run fast.

Dunbabin 2007 modeled this by simulating the growth of plants with 3-d models of root systems in order to examine sensitivity of uptake of water, nitrogen, and phosphorus to variation in key root parameters.

Looking at what parameters are important when crops are competing against weeds, here's what Dunbabin says about that:

"the ability to quickly (growth rate) and effectively occupy (rooting density) the soil volume during crop establishment, may be important for denying weeds water and nutrients, thereby conferring competitive ability"

When there is no competition between crops and weeds, effective exploration is important:

"The ranking of P uptake efficiency as important for the acquisition of mobile nitrate and water
resources by weed-free crops...suggests that foraging for the least mobile, and often most limiting nutrient, may provide the best strategy for acquiring all soil resources (Robinson, 1996a)."

Here, the modeled plants are growing in relatively low-P soils, so to acquire the most water, you have to have a big plant. Having a strategy for effective acquisition of P becomes the most important parameters there.

One parameter not important regardless of whether there is competition or not? Potential transpiration rate.

Water is a mobile resource, but roots still have to wait for water to move to them.

Considering that nitrogen uptake kinetics aren't important for nitrogen competition, and mass flow is slower than diffusion, this makes sense.

It is important to note that the arena of competition is important here. The plants were started from seed (I think) and allowed to grow for 12 weeks, simulating a quick crop rotation.

The question here is what aspects of roots become important when competition is not a 12-week race? What becomes important when perennials occupy the same space for years? And if nutrients aren't limiting? Then what?

What does the optimal root system look like for plants growing in the absence of interspecific competition when water is limiting, but nutrients aren't?

A few thick roots?

Many thin roots?

Unknown.

Exploring competition for water

From Lobet et al. 2014

It is true that drought kills plants. 

Drought lowers soil moisture. Low soil moisture kills plants. Therefore, drought kills plants. 

Yet, the rate at which drought lowers soil moisture is dependent on the plants that are present in soil. 

Plants lower soil moisture. Low soil moisture kills plants. Therefore, drought kills plants. 

Therefore, it is also true to say that plants kill plants. 

And when plants kill plants by using resources, that's resource competition. 

There has been a lot of great work over the past decade examining the mechanisms of how drought kills plants. 

But not so much on how plants kill plants when water is limiting. 

About a decade ago I was curious about some of the mechanisms of how plants compete for nutrients.

To explore this, I put together a model...actually I asked Trevor to put together a model...to simulate the movement and uptake of nutrients in soils.

This model was parameterized at a fine scale and could simulate the supply, movement, and uptake of nutrients in soils. 

It was able to show patterns of nutrient distribution in soils like this.. 

2 cm x 2 cm cross section of soil with all roots orthogonal to the plane. Red indicates high nutrient concentrations in soil solution. Blue is low.

With the model, I was able to show that plants acquired nutrients in proportion to the fraction of all the root length they had in a given volume of soil. Plants had a lot more roots than they needed to take up nutrients...if there was no competition. Once more than one plant had roots in a given volume of soil, a race set in.

As a result, plants can have 1000 times more roots that is optimal for maximizing growth.

That all pertained to nutrients though.

I'm curious about how competition for water works.

For example, does competition for water favor plants with high root length density? Would this also lead to a race like nutrients.

For competitive purposes, is there any benefit to being able to sustain a low minimum water potential? Under what conditions, if any, does drought tolerance affect competitive outcomes?

I'm also curious about the interactions between nutrients and water. Does increasing transpiration rate help with nutrient competition? Do dry soils exacerbate nutrient limitation?

But first, I need to adjust the model to handle water.

That means making soil moisture dynamic, parameterizing water fluxes between pixels and into roots.

The hardest part of all of this is figuring out how to parameterize water uptake by a  given root. There is no simple Michaelis-Menten equation here. Roots are a 1000 connected little straws

Still, I've been impressed by some of the developments in root modeling over the past few years.

I can expand on that later.