Tag Archives: Plants

Accidental Ferns

I have this moss terrarium that is not doing that well.  It’s never done well.  I guess moss doesn’t really want to live in a jar.  Probably more than a year ago, I dropped a maidenhair fern frond in there that was loaded with spores.  I thought it might sprout, but after the leaf decayed, nothing happened so I forgot about it… not that I really knew what fern sprouts looked like.  Months ago, I started seeing this strange structure growing out of my dying moss clumps.  It kind of looks like tiny kelp.  I thought maybe it was a liverwort or some moss structure that grows from moss in some last attempt to live.  My “moss kelp” eventually grew some branches, so I thought it was making spores.


From left to right: some scraggly moss, young maidenhair ferns, and the fern prothallia

Fast forward to today.  My maidenhair fern in my office (a division of the one mentioned earlier) is dropping spores all over the window sill, so I did some internet research on how to grow ferns from spores.  That’s when I discovered I’ve actually already done it.  The “moss kelp” is the prothallium or the gametophyte of the fern (the structure where fertilization happens).  From the prothallium, the fern that we recognize grows.  Now I wonder if I can do it again on purpose.

A note on the photograph: photographing prothallia is really difficult.  I was frustrated at the lack of good photos online, but now I understand, so please excuse my lack of detail in my photo.  I may try to get some better macro photos later.

Spatially Enabled Zotero Database

As a geographer, I’m a visual person.  I like to see distributions on a map and where things are matters to me.  A few years ago, while I was writing a paper I became overwhelmed with trying to remember the locations for the studies I had read (for coastal plants, latitude matters), so I started marking the locations of studies on a map and eventually turned it into a printed map.


But adding new studies and sharing the results is a cumbersome and the spatial data is largely separate from the citation information.  So I set out to find a way to store spatial information in my citation database and access the spatial information for mapping purposes.  The end result (which is still a work in progress at press time) is a web map of coastal vegetation literature that updates when new citations are added to my Zotero database online.


How I Did It:

Key ingredients: Zotero, QGIS, Spatialite, Zotero Online Account

I started working with the Zotero database I already have populated with literature relevant to my research on coastal vegetation.  I moved citations that I wanted to map into a separate folder just to make the API queries easier later.  I made a point in a shapefile for the location of each study using QGIS.  I gave the attribute table fields for the in-text citation and a text description of the location for human-readability, but the most important field is the ZoteroKey.  This is the item key that uniquely identifies each record in the Zotero database.  To find the key for each citation, in your local version of Zotero, right click on the record and pick “generate report”.  The text for the key is after the underscore in the URL for the report.  In the online version, click the citation in your list.  The key is at the end of the URL in the page that opens.


My map only has point geometries right now, but that will change in the coming weeks.

The spatial information was then to be added to the Zotero database (specific queries can be found on GitHub) in Spatialite.  The Zotero schema is quite large but not impossible to navigate.  Currently, there is no option to add your own fields to Zotero (I tried… I failed… they tell me the option is coming soon) so I put my geometries into the “Extra” field.  Using Spatialite, I opened the Zotero database and imported my shapefile of citation locations (having new tables doesn’t break the database, thank goodness).  Then I removed any existing information in the “Extra” field and filled it in with geometry information in the style of geoJSON.  The string looks like this:

{"type": "Point", "coordinates": [-123.069403678033, 38.3159528822055]}

After updating the citation records to house the geometries, I synced the changes to my online Zotero repository from my desktop program.  Now it’s ready to go into a web map using the Zotero API.  My webmap code can be found in my GitHub Repository.

What’s Next?

I would like to develop a plug-in for QGIS that makes adding the geometries to the Zotero database easier because not everyone wants to run SQL queries on their active citation database that has been years in the making (I backed mine up first!).  The interface would show the citations you want to map, then users would pick a citation, then click the location on their QGIS project where the citations should be located.  The plug-in would insert the corresponding geometry for them.

Dance + Science = Fun + Learning

I realize my post title is not longer true once you rearrange the equation, but you get my point.  Science really can be fun and easy when you add an unexpected twist like dance or other forms of art.  That’s sort of the idea behind the “Dance Your Ph.D.” contest organized by Gonzo Labs.  Having just finished a dissertation and being a dancer, I really wanted to enter this competition, so I gathered up as many people as I could and made it happen.

One important theme of the dance work that I am involved in is the idea that anyone can dance at any age and even that limited physical ability shouldn’t limit you from expressing yourself through movement.  Given that idea, I didn’t restrict my cast to only dancers.  I ended up with a cast and crew of about 30 men and women ranging from 5 to 80+ years old, some dancers and some not.  The key to success in this situation is that I chose a dance form that anyone can learn quickly, in this case, it was improvisational modern dance.  Simple, repeated movements through space performed en mass are sometimes quite mesmerizing and anyone can do it and look good.

The group also had varying experience with science concepts.  A handful in the crowd have PhDs in a scientific field, some of them work with scientists, some are artists or accountants or philanthropists, and some are kindergarteners.  However, with the exception of me, no one understood my dissertation chapter nearly as well as I did, so everyone needed a science lesson.

Learning how to do the improvisation and the rules behind the movements didn’t take long – maybe 20 minutes.  And all together, the whole filming took less than 3 hours.  The preparation on my part was significantly more than that, but that’s the case with any dance performance.

In the end, I think everyone learned quite a bit both about art and science.  And it was fun!  It was amazing to work with such a diverse group of people on this kind of project.  I am in complete awe of their patience with the process, their willingness to give their time, and of their open hearts in general.  I’d like to do this again some time, but we’ll need to come up with a new science concept to dance.

Here is my entry for the competition (I already know about the typos):

Click here for my research YouTube channel.

Please Don’t Flower!

For many bulbs, spring is the time to come back to life and show off with big showy flowers.  For my amorphophallus bulbs, it’s also time to awake from their winter slumber, I just hope beyond hope that they don’t flower.  Why?  Because they’ll stink… like rotting meat.  I’ve never seen them do it, but it doesn’t sound pleasant.  These are a cousin of the huge rotting corpse flowers you hear about (UC Davis has one and so does the Huntington Library) and while these ones are much smaller, I think even having a small rotting hunk of meat in your yard would be unpleasant.  Now, they don’t flower every year, only when they store up enough energy.

The big one I’ve had for four years.  I received it from a student who brought free samples of the plant he was giving a presentation on.  The little one showed up last year, apparently spawned from the big one.  It was a nice surprise to get a new one and not have to go through the flowering process.  I’m wondering though, if the big one had enough energy to make a clone last year, is it going to flower this year?

This year I re-potted them in their own pots and started watering them again last week.  If they decide to flower, the flowers will come up first, then the leaf.  Yes,  they’ll only put up only one leaf.  It will be a pink-ish stalk with purple spots a little less than knee-high topped with an umbrella-like leaf.  When the leaf dies back in the fall, I’ll stop watering them and put the pots away where they’ll be safe.  Then when spring comes again, I’ll start watering them and hoping they don’t decide to flower.


Annoying the Garden Variety HOA

My garden plot.

Just because it's not pretty doesn't mean it's not working.

You might think a community garden is a free-for-all — a bunch of hippies growing what they want, however they want, encouraging innovation and creativity.  Oh, you’re so wrong.

I’ve been gardening in a 20 x 20 foot garden plot at in a community garden for the last 5 years.  It’s not an ideal space.  My plot’s got about 90% shade in the summer and a healthy population of furry beasts (ground squirrels, tree squirrels, and a gopher for the triple threat).  Gardening is not easy in this space, but I’m succeeding anyway.  The trouble is, it doesn’t look like I’m succeeding.  I’ve been threatened 3 times in the last 2 years that if I don’t make my garden look like a garden, it’s going to be taken away.  That’s sad because I think I’m getting more food from my mess of a plot than many of the ones that look nice.

Here are some of my gardening policies that lead to conflict with the community garden’s established rules and desired aesthetic:

  1. If a plant comes up in a spot, it’s a good spot.  Leave it.  Yes, it might be in the middle of what I thought was the path, but clearly, the plant likes it there or it wouldn’t have germinated.  Work around it.  It won’t be there forever.
  2. Cover, even if it’s grass or dead plants, is a good thing if you have squirrels.  Squirrels don’t eat grass, so if your food plants are hiding in the grass, they are more likely to be overlooked than if they’re out in the open.  Just pull the grass before it goes to seed.  Cover can also take the form of dead plants.  I leave my arugula stems in place once they’ve died.  It keeps the critters out.
  3. If one kind of plant gives you trouble, forget it.  Pumpkins and squash won’t grow in my plot.  I’ve tried time and time again.  After a few years of trying, it’s time to move on.
  4. Find the plants that do work and focus on those.  I’ve found that I am completely successful with mint, oregano, rosemary, arugula, broccoli raab, green onions, and artichokes in my plot.  And as long as the gopher is busy somewhere else, I can get big onions and garlic.  That’s not really that bad of a spread.  You can always trade for the things you want (like pumpkins).  One year I had so many artichokes, I had to give them away.  And that was from just two plants.  It’s not hard to find homes for artichokes though.
  5. If something works, save some seeds.  Yes, it looks ugly to have a bed of bolted leggy arugula for a few months, but these are the plants that did well, so why not re-plant them?
  6. Don’t rake and don’t till if you’ve got bad soil.  No amount of compost is going to fix the solid clay I’m working in.  Leave the organic matter on the top.  For example, leaves are excellent for soil improvement.  The trouble with mixing things in is that the good stuff gets diluted.  Start improving the top and eventually, you’ll get a thick layer of good soil.  I’m not there yet, but I’ve seen improvement already that’s pretty encouraging.
  7. Plant weeds.  You can eat all kinds of stuff that’s considered a weed — arugula, dandelions, and mustard are just a few of the foods considered a weed in my community garden.  Every time I get one of those emails telling me to clean up my plot, I remind the coordinator that I plant weedy-looking plants on purpose.

So if you happen to coordinate or oversee a community garden and you happen to have a misfit plot, perhaps talk to the owner of that plot and see why they do what they do.  Maybe what looks like a mess is actually a decent strategy for dealing with difficult conditions.  Maybe you can get some tips.

What kinds of unconventional methods have you tried in your garden?

DIY Indoor Pond Creatures

Trumpet snails are cool in their own way, but ghost shrimp are majorly entertaining.  They’ve got some spunk, that’s for sure.  I recently picked up three ghost shrimp to add to my indoor pond.

It already had trumpet snails, but they really aren’t that exciting.  I mean, if you pay close attention, they can be quite funny at times, but mostly they just glide around the tank like pointy-ended roombas.

A big trumpet snail.

The shrimp are perfect companions for the snails.  They add a bit of flair because they can swim through the water column.  They move around a lot, looking for food constantly.  If they come across a snail, they tug on it with their claws, which makes the snails jerk away like they are grumpy and don’t want to be bothered.  The shrimp are mainly detritivores, so they aren’t likely to hurt the snails.  I think if they got a tiny one, they might eat it, but one or two lost isn’t a big deal.  I don’t think I’m going to have to feed these guys directly either since the plants seem to provide more than enough food for the snails.

There really only is one problem.  What do you name 3 shrimp?  Ideas are much appreciated.

Ghost shrimp are hard to see and even harder to photograph.

Beach Plant Competition Diagram

Nothing’s better than a diagram for an explanation, as far as I’m concerned.  This is a diagram I drew for a talk about beach plants (shocking, I know!) for the BEACH Ecology Coalition meeting last year.  It explains where we expect plants to compete with each other.  Again, this was made with Inkscape, my favorite vector illustration software.