Wednesday, May 28, 2014

Improvements on measuring drought tolerance

Just a quick note here on measuring drought tolerance.

In the past, we were using a pressure bomb to determine a plant's water potential at which stomatal conductance falls below a threshold (5 mmol m-2 s-1).

Using a pressure bomb on grasses can be tough. They are often just a few mm across and don't have that much water in them. Magnifying glasses just don't magnify enough.

I dug around a bit and bought a digital microscope. Turns out these work great.

First, we lock in the grass blade at a pretty high height. Note we spray painted everything black to reduce glare.

Then we place the microscope camera near the blade. The scope camera is 5 MP which gives fairly good resolution. A Macbook Pro with a Retina display is high enough resolution to show things well (most laptop monitors are only 2 MP).

The scope camera is under $100 at Amazon.

After that, we pressurize and wait for the water.

Holding things still can be problematic, but it's working pretty well to be honest. Also, what we see on the screen is a bit higher resolution than this video for some reason.

Much better than magnifying glasses.

Saturday, May 24, 2014

Bison weight trajectories

Weight trajectories of 16 bison at Konza Prairie. Colors don't mean anything here.

More and more animals are walking over the bison scale. I think because of what watersheds were burned, the bison have just been in other parts of Konza. Only about 80 of the 120 animals that have a tag have walked over it since we installed it about a month ago. We have a lot of other weights, but they most likely are for other animals that didn't get tagged (or ones with a tag that didn't get an EID reading).

Still, we're just now getting enough data to start to see some trajectories of weight gain.

Over the past month, there are the 16 animals that we have enough data for to start to look at weight trajectories...I've scrubbed out the animals with too few data. Data points that are obviously too low/high have also been removed.

The general trajectory since we installed the EID reader on May 1 has been for animals to be gaining weight.

Yearlings are gaining 1.3 kg a day.

2-year olds are gaining 1.6 kg a day.

The two older animals 1.9 kg a day (take with a grain of salt).

2-3 lbs per day is a pretty reasonable number.

Friday, May 16, 2014

Note to myself on standard errors

1.96 is well known, but not the others...

Found this here.

Confidence levelStandard Errors from mean

Friday, May 9, 2014

Two innovations for scientific projects

Two good innovations for productivity lately.

1) Basecamp. I've tried different project management systems over time. Basecamp is pretty good. It's web-based. It allows unlimited users for a set number of projects. It takes care of to-do lists, calendars, discussions, and files. If you have more than 2 people on a project, I'd recommend it. $20 a month is a bargain. This isn't lab-management software, but is a good generic format for projects.

2) Filemaker + iPads. Data entry can be tough. Writing things down can be laborious and introduce transcription errors. For the new project, we've deployed a Filemaker database on the iPads for data entry. Depending on the task, there is a separate data entry window. Syncing can be a bit clunky, but it essentially requires moving the database file to a master computer and then importing the data. Still, this is a scalable approach that let's us record a lot of data and store it in a central database. A big improvement over past options and good enough for who it's for.

The iPad would be even better if we could use barcodes. Just not an option right now. Instead I introduced 4-character unique codes for all of our samples. Each iPad has a keyboard cover that  facilitates data entry. Instead of entering long strings of numbers, a 4-character code is entered. Filemaker checks to make sure it is in the database to reduce any entry errors.

Thursday, May 8, 2014

Schism over nature conservation

The May 12 New Yorker had a well-written piece on the Nature Conservancy. In a concise fashion, they frame the debate over nature conservation well.

On the one hand, there is the current head of TNC (Mark Tercek) and its chief scientist (Peter Kareiva) advocating for nature conservation through economic valuation.

On the other hand you have ecologists like Michael Soulé and Reed Noss who believe that the value of nature transcends economics and should be conserved independent of economic valuation.

The economic valuation approach lead to partnering with Fortune 500 companies to reform their practices in favor of conserving nature where economics align. It produces books entitled Nature's Fortune.

The transcendent approach works with individuals and governments to conserve Nature for its own sake. It produces books entitled Nature's Keepers.

The inside view of the debate is enlightening.

Both approaches should coexist in the world, but you wonder if they can coexist in the same organization.

Answering this requires answering whether economic valuation and transcendence reinforce one another or are they antagonistic?

That calculation might be even too hard for the economists.

Tuesday, May 6, 2014

Developing model species sets

A bunch of us put together a manuscript laying out the framework for developing model species sets.

Reviews are back from the first journal to which we submitted this. And they are interesting.

On the one hand, reviewers considered the idea "thought-provoking" and actually asked us to be even bolder.

The criticisms mostly came from the editor.

Concerns for the model species set primarily revolve around the consequences for selecting a model species set that isn't random. How much will this bias our understanding of the relationships among plant species traits?

The counterargument for this is that any sampling scheme currently being used is not random.  And the consequences for lack of randomness can be tested with further specie selection.

Also, apparently there are concerns about the consequences for selection model species that parallel concerns for model organisms.

But no one would ever go back in time and prevent model organisms from being established.

In all, model species sets are going to be important. They really are the only way to begin to examine how broad suites of species traits relate to one another...

This will be interesting.

Sunday, May 4, 2014

Communication in a divided world: reinforcing insularity

A new piece I wrote just came out in Nature Geoscience.

It's a commentary that covers some of the impediments to communicating global change science.

I focus on climate change and ranchers, but there are some broader messages to take away here.

For me, the novel nugget here was the idea of reinforcing insularity. The social networks of individuals can reinforce an understanding of a topic in a way that can be hard to disrupt.

For livestock managers, there are a number of interactions that can reinforce a set of views on climate change. Ranchers have a set of views and these can be reinforced by what media they consume, while media outlets tailor messages to their audience. Ranchers also influence their governmental representatives, who draft policies that reflect the opinions of their constituents.

Still, the message is hopeful. A number of instances show that there might be more alignment of interests than has been commonly recognized.

Reproducibility: "even the paint on the walls"

I remember reading a book that talked about reproducibility. Part of the story was that some techniques are so sensitive and so complex, that once they are successful, you don't vary anything when reproducing it. One of the references was a microchip plant, where once successful, they would reproduce the conditions exactly, "even the paint on the walls".

We're starting up the first round of water potential measurements for the GD3D project. We'll measure psi-crit for over 1000 species. The protocols are almost exactly the same as last time I tried this, but a few changes ensued. For example, different growth chambers.

In the technique, we stop watering the plants after 6 weeks of growth and then measure stomatal conductance every day (or more). When gs < 5 mmol m-2 s-1, we measure the plant's water potential.

The first set of plants I was measuring seemed drier than before. For a number of them, I couldn't push out any water. I checked on the numbers I had last time for species that had overlapped and it seemed like plants were drier than last time.

I went through the possible culprits. Turns out it was the machine.

I used the same model machine as before and it had just been calibrated. But, it was a different machine. I just picked up the other one rather than the old one,  which had been calibrated at the same time.

I did a comparison of measurements between the two on the same leaves.

The other machine I was using was reading conductance twice as high as the original. No idea why that would be, but it was pretty clear.

So, what was 5 mmol m-2 s-1 on the old machine was 8.5 on the new one. 5 on the new one would have been 3 on the old one.

That's why they were so dry this time.

I changed the paint on the walls.

I've got some plants to regrow.