Research update: February 2017

 

Just a quick update here for February. Although we got no snow cover (no February snow in Chicago – can you believe it? I wonder how the green roof plants will do after this unusually warm winter!) it was still a good time to get some indoor work done. This past month, that meant more writing and lab work.

 

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Which offspring do I have enough genetic data for? Color-coded charts help me figure out which samples I need to run next in the lab. 

 

My February writing mostly focused on a manuscript I’m writing about the different types of plants that survive on green roofs over long periods of time. I used some long-term plant surveys of 6 green roofs in Germany and included a plant survey I conducted on 13 green roofs in the same region when I was there back in 2013. While I was writing, I was also analyzing the collected data to see if the types of plants that arrive on green roofs right after their planted are different than those that end up staying there for a long time. I did find some differences. It turns out that weedy plants able to spread seeds and easily use resources like water and soil nutrients are common on green roofs for a few years after they are built. But later, only the species that have traits that make them tough enough to withstand the heat and drought on green roofs will remain. It took a long time to figure this out and write up the manuscript. I now have a draft. I’ll keep working on this manuscript and will hopefully be able to submit it to a journal for publication review sometime this spring.

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More little test tubes of DNA and more genetic sequencing in the lab. I’m getting more data every month but still have more to collect.

In between writing, I also got in a little bit of work in the genetics lab. I’m still trying to figure out how much genetic diversity the plants on the green roofs have. When I have some more data, I’ll figure out if this is similar to plants that have been living on the ground for a long time. I’m hypothesizing that the plants on the green roofs don’t have as much genetic diversity because there are fewer pollinators there so the plants that can breed with themselves, do. I’ve been collecting the data for this experiment for a while now. I think I’m getting closer but will still be spending more time over the next month or two working with machines in the lab that help me make copies of my plants’ DNA and then determine their genetic sequences.

Other than the writing and lab work, I did get to present some of my work at a local conference in February. The Chicagoland conference was called WildThings and brought together over 1,000 people from the area who are interested in conserving the wild plants, animals, and other critters that we share our space with. The presentation went well and the presentations that I got to see were very interesting too. I especially liked learning more about conservation efforts that are happening in the corner of the world that I call home.

Next month: more writing and lab work!

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Research update: January 2017

Happy New Year and welcome to year #6 of my research blog. I think it’s going to be an interesting but different year as I transition from conducting research as a graduate student scientist to… well, a regular scientist! For one thing, I won’t have any of the typical field work during the summer that I’ve always had in the past. I’m sure I’ll still get out on the green roofs now and then but just without all the data collection. Instead, I’ll be doing a lot more data analysis to determine what all of my past data mean and I’ll be writing a lot about my conclusions. That, and applying for a new job where I can continue to do even more research in the future!

 

A new year means it's time to clean out old samples from the freezer and make way for the new ones. Say goodbye to thousands and thousands of little bits of now useless DNA.

A new year means it’s time to clean out old samples from the freezer and make way for the new ones. Say goodbye to thousands and thousands of little bits of now useless DNA.

 

In January, although the plants on the green roofs weren’t covered in snow for even a single day (in Chicago – can you believe it?), I still spent all my research time indoors. I spent most of my time writing. Specifically, I worked on manuscript revisions for an article I’m writing about the data I collected on the green roofs in Germany back in 2013. After writing this article last summer and submitting it to a journal for review, I received comments back from the scientist reviewers. I needed to make a lot of little changes and a few big ones before the journal would consider publishing it in a special issue about green roof ecology. It was a lot of work to complete all the changes and defend some of my methods to the reviewers, but I’m happy to say that all the effort was worth it and the manuscript has been accepted for publication! Now I wait for the editorial process to continue. I hope the special issue of the journal is complete and published by this spring. It seems like these things can sometimes take a very long time.

Aside from the manuscript revisions, I’ve also been writing little sections of four other manuscripts that I have yet to finish and submit. Each of these papers is a chapter of my dissertation. They are all in various stages of completeness. When I decided to become a botanist I didn’t realize just how much writing was involved. Now I have to set reminders on my watch just to remember to get up from my desk and take writing breaks every couple hours. It’s a different kind of work from the data collection but it really helps me solidify my thoughts and explain the results of my experiments. I’m looking forward to meeting my weekly writing goals and completing more manuscripts in the future.

I was one of the keynote speakers at the dinner for the Presidential Fellows at Northwestern University in January.

I was one of the keynote speakers at the dinner for the Presidential Fellows at Northwestern University in January.

In the middle of the month, I took a break from writing to prepare and give a presentation at a dinner held for the Presidential Fellows at Northwestern University. This group of scholars comes from all of the departments in the graduate school so the audience has a wide variety of backgrounds; both science and non-science. It’s a different kind of presentation to give because I needed to talk about the merits of my research but in a way that anyone could understand. It was a little nerve-wracking but it went very well and I’m glad it’s over!

It worked! I look at the height of some blue peaks on the computer screen that help me determine the genetic makeup of all my plant samples. It feels so good when all the machines work and I actually get some data.

It worked! I look at the height of some blue peaks on the computer screen that help me determine the genetic makeup of all my plant samples. It feels so good when all the machines work and I actually get some data.

And finally, January was also filled with some lab work. (No surprise there!) I’ve been having some troubles getting some of the equipment to work so in January, I re-ran a lot of my samples through the genetic sequencing machine. I never have 100% success but I was able to collect a little more data for some of my samples. Over the next couple months, I’ll keep trying to get a little bit more and a little bit more but by the end of March I think I’ll just have to make do with what I have. Hopefully next month I’ll have some good news to report on this part of my research. Fingers crossed!

Research update: November/December 2016

The fall sun sets over the dormant plants on a green roof. See you next spring, plants!

The fall sun sets over the dormant plants on a green roof. See you next spring, plants!

In my previous post, I started by saying that I was gearing up for a winter of lab work, data analysis, and writing. In between holiday gatherings and celebrations (GO CUBS!), my work predictions for November and December were pretty accurate.

I remove the sealed top from my tray of samples after the DNA has been copied. It may not look like a lot of liquid in there, but there are thousands of copies of DNA!

I remove the sealed top from my tray of samples after the DNA has been copied. It may not look like a lot of liquid in there, but there are thousands of copies of DNA!

I drop oil on top of my samples in the little wells before running the final step of my paternity experiment. Then I cross my fingers that everything works this time.

I drop oil on top of my samples in the little wells before running the final step of my paternity experiment. Then I cross my fingers that everything works this time.

A renewed focus on lab work was my biggest priority over the past two months. I’ve been having a difficult time collecting all the data I need for this portion of my research due to a variety of factors including bad reagents (chemicals), low DNA quantities, low genetic diversity in my samples, faulty equipment, running out of supplies, dwindling research funding, possibly some unknown errors on my part and maybe even just some bad luck. (The lab manager also suggested that gremlins might be coming into the lab at night to mess with my experiments… at this point, is anything possible? Who knows!) So I’ve been fighting the good fight and filling in the missing data a little bit at a time. Sometimes it feels like I’m putting together a 1000 piece puzzle one piece at a time. It’s very arduous and I don’t know what the finished product will look like but I’m getting there and can’t wait to see the final results! In the meantime, I’ll keep on extracting more DNA, amplifying or making copies of the DNA, conducting the paternity tests, and looking for patterns of genetic diversity in the plant populations on my green roofs. You’ll no doubt hear more about these tasks during the next update.

I use this helpful pipette to transfer multiple samples at a time as I load the next yellow plate for DNA copying. Lots of the lab procedures are repeated over and over again.

I use this helpful pipette to transfer multiple samples at a time as I load the next yellow plate for DNA copying. Lots of the lab procedures are repeated over and over again.

This is what it looks like when you wait too long to collect your soil samples from your green roof experiment and have to do it when it's really cold outside!

This is what it looks like when you wait too long to collect your soil samples from your green roof experiment and have to do it when it’s really cold outside!

When I needed a mental break from the lab work, I mostly kept busy indoors. There was one chilly day that I spent on a green roof collecting some soil samples for a later analysis in the lab. I could have collected the soil back in October when temperatures were still balmy but this task slipped my mind and I ended up getting the job done on a very windy cold November day when the wind chill was about 20 degrees F (that’s about -7 degrees C). At least it wasn’t snowing yet! Other than that, I spent a lot of time analyzing the data that I’ve been collecting from the green roofs over the past few years and starting to interpret the patterns that I’m seeing. After having some initial data interpretations, I spent two weeks in December in a dissertation boot camp. This boot camp is a quiet place for doctoral candidates like me to really focus on writing about their research. It’s a great way to get some encouragement from peers to accomplish some writing before taking a little holiday break.

Another set of 96 samples is loaded up and ready to be processed in the DNA sequencing machine. This is the step in the paternity test where I determine each sample's genetic fingerprint... if it works correctly.

Another set of 96 samples is loaded up and ready to be processed in the DNA sequencing machine. This is the step in the paternity test where I determine each sample’s genetic fingerprint… if it works correctly.

As the year came to an end, so did my mentoring with the PlantingScience project. This program matches up thousands of students with plant science mentors from all around the country. As a liaison and scientist mentor for the project, I helped high school students and their teachers learn about “The Power of Sunlight,” or how plants perform photosynthesis. As a previous high school teacher myself, it was great to get to interact with this group of students and see how the teachers were using technology to introduce students to a diverse group of scientists. Who knows, maybe some of these students are now budding plant scientists!

Dried leaves rest among the last sprigs of green on top of a green roof at the Chicago Botanic Garden. Snow is coming soon!

Dried leaves rest among the last sprigs of green on top of a green roof at the Chicago Botanic Garden. Snow is coming soon!

Research update: June/July 2016

Well, as you can see, my “monthly” research updates are a little bit behind and this post is extra long. It seems like with all the work to be done outdoors and out of town, it’s been hard to sit down to write about it all. But as I look back at June and July it’s exciting to remember all that has happened.

Ratibida pinnata (gray-headed coneflower) blooms beautifully in one of my green roof plots.

Ratibida pinnata (gray-headed coneflower) blooms beautifully in one of my green roof plots.

First, I am happy to say that an article I wrote about biodiversity on green roofs was published in Wild Seed Magazine, a publication from the Maine-based non-profit Wild Seed Project. I won’t say too much about the article, other than you should click HERE to read it and if you should click on the link above if you want to get a copy of the whole magazine (which includes an article from the amazing naturalist Doug Tallamy and is really good).

The Dalea purpurea (purple prairie clover) was blooming on the green roofs in June and attracting pollinators!

The Dalea purpurea (purple prairie clover) was blooming on the green roofs in June and attracting pollinators!

As far as research goes, June started out with data collection on the green roofs. I’m continuing to measure the plants in the prairie mixes that I planted back in 2012 and at the beginning of the summer, things looked a little sparse but promising. After a pretty rainy summer, some of the same plots are actually pretty lush and there are many species of plants that are flowering in beautiful displays of yellow, white, and purple flowers. It’s impossible to capture them all with my cell phone’s camera, but believe me when I tell you that they are lots of pollinators coming to visit my plants too! When I’m back to more indoor work in the fall I’ll analyze the data to look for significant patterns. So far, it looks like the species from the prairies that are most similar to green roofs are the ones that are growing the best. It’s really exciting for me to know that when I stop collecting the data for this experiment, there will be some little prairies on the green roofs for years to come.

I'm continuing to measure the amount of water that the different plant combinations capture and hold throughout the day.

I’m continuing to measure the amount of water that the different plant combinations capture and hold throughout the day.

I continue to measure the growth of the plants in my green roof prairie plots that I originally planted back in 2012.

I continue to measure the growth of the plants in my green roof prairie plots that I originally planted back in 2012.

My experiment measuring water capture continues as does my collection of weeds from the green roof trays to determine how good the prairie plants are at resisting weeds compared to succulent plants. Everything is going well with those experiments except for the fact that a surprise thunderstorm messed up some of my data and I have to do one part of the experiment over again. I’m not happy about that, but that’s just how botanical research goes sometimes. I’ve got my fingers crossed for some rain-free days in early August.

Weighing the weeds continues. So far it looks like the succulent Sedum plants are the best at preventing weeds.

Weighing the weeds continues. So far it looks like the succulent Sedum plants are the best at preventing weeds.

 

Back to the ground - I finally found the Penstemon plants I was looking for in the shortgrass prairies. It's fun to go back to the sites that I'm trying to replicate on the roof and appreciate how special these habitats are.

Back to the ground – I finally found the Penstemon plants I was looking for in the shortgrass prairies. It’s fun to go back to the sites that I’m trying to replicate on the roof and appreciate how special these habitats are.

Pollinators are visiting my plants on the green roofs! It's exciting to see evidence of the ecological relationships that I was hoping to support.

Pollinators are visiting my plants on the green roofs! It’s exciting to see evidence of the ecological relationships that I was hoping to support.

In addition to the green roofs, I also went to a couple prairie remnants southwest of Chicago to collect some plant tissue. I’ve been putting my lab work on pause for the summer, but if you remember, one of my experiments is to measure pollen movement between green roofs using a paternity study. Well, I’m finding that it’s really hard to distinguish one “dad” plant from another because the dads have very similar DNA. I think this is because the nursery where I got the experimental plants wasn’t using a diverse mix of parental plants but I want to make sure that the plants you’d find in nature would actually have more diversity in their DNA. To do this, I need DNA from plants in their natural habitat – and this is what led me to collect leaves from the shortgrass prairies on a steamy Friday in June. I was hoping to find three whole fields full of my target species of Penstemon plants but, after hours of searching, I only found two small patches. For now, I’ve collected the leaf tissue and it’s drying in the lab. I’ll get back to that when it’s time to get back to the lab in the fall.

Lespedeza capitata (roundhead bushclover) blooms beautifully in one of my plots on a green roof.

Lespedeza capitata (roundhead bushclover) blooms beautifully in one of my plots on a green roof.

It’s actually hard to believe that I was able to collect so many data when I look at all the times I was out of town, talking about research rather than actually conducting it. But through these experiences, I met a lot of wonderful people that are also interested in plant and animal conservation, urban ecology, and science education & communication – my favorite things! At the beginning of June, I was thrilled to be selected as a participant in ComSciCon in Cambridge, MA. This is a graduate student-run conference for other graduate students in science who are interested in engaging with non-scientific audiences. The fellow attendees I met are involved in some amazing endeavors, including documentary filmmaking, graphic design, afterschool programs, and policy advocacy. I could go on for many paragraphs about how awesome these folks were, but I’ll just summarize by saying that I was truly inspired. I started writing a piece about green roofs to be submitted to a children’s magazine while I was there and I’m hoping to get it published this year – stay tuned.

After my trip to the East coast, I headed out west to Colorado Spring to participate as a botanist mentor in a workshop called Digging Deeper. As a mentor, I got to meet high school teachers that teach their students about plants together with plant scientists in a program called Planting Science. As a previous high school science teacher and current scientist, it was really fun to try and figure out the best ways to teach teenagers about plants in an exciting and engaging way. In the fall, I’ll be a mentor to a couple student groups and through video conferences and email messages, we’ll help them design their own experiments to learn about botany – how cool is that?

A spontaneous Penstemon plant (the one I'm studying in a different experiment) has germinated and flowered in my experimental green roof trays. I'm glad to see that this native species does so well on green roofs.

A spontaneous Penstemon plant (the one I’m studying in a different experiment) has germinated and flowered in my experimental green roof trays. I’m glad to see that this native species does so well on green roofs.

I had a couple more trips a little closer to home too. The first one was to Michigan to share my research and meet the new cohort of Northwestern University Presidential Fellows. Wow. More amazing people doing some fascinating research from applications of nanofluids and deciphering the genetic code to impacts of affirmative action on hiring practices in the NFL. The second trip was to Wisconsin to give a presentation at the North American Congress of the Society for Conservation Biology. I’m pleased that my presentation about my green roof research was well received and I even got to meet some other professional from the Chicago area that work with trees, wildlife, and the human-nature connection. As I finish the last year of data collection for my dissertation, it’s really helpful to start thinking more about the broad applications of my research and how the things I’ve learned so far might be applied to other fields when graduate school is complete.

As a final note, in addition to the research and trips, I also got married in July! Did you notice the new name of the site? I may have a new name but the research is still pretty much the same – I don’t think the plants noticed at all!

Up next month: Field work, lab work, data analysis, writing, and even maybe a TV appearance!

 

 

Research update: January 2016

Winter = writing & lab work. After a few years as a botanical researcher I’m beginning to really understand this seasonal work pattern. So that’s what my January looked like. I spent time making revisions to a research report that I’ve been working on for a while now. This particular report keeps getting better little by little but it is quite a process to take years’ worth of work and write a technical yet brief summary of what it all means and why it all matters. It’s getting there!

Tiny seeds on agar plates experience simulated spring in an incubator.

Tiny seeds on agar plates experience simulated spring in an incubator.

I spin the small tubes filled with DNA and chemicals in a centrifuge to separate the layers and help purify the DNA

I spin the small tubes filled with DNA and chemicals in a centrifuge to separate the layers and help purify the DNA

Lab work has also taken on some different forms and was in full swing in January. In one part of the lab, I washed soil off of the roots of weeds collected from my green roof plots. The clean weeds were then dried in an oven and weighed to compare how much weedy plant tissue (called “biomass”) grows in traditional succulent green roofs compared to my prairie-style green roofs. In another part of the lab, I continued to extract DNA from some tiny plant seedlings for a different experiment. This DNA will later be used to measure how pollen moves between green roofs.

I use this computer hooked up to a fancy machine to determine if my DNA primers are working to make lots of copies of the DNA from my plant seedlings.

I use this computer hooked up to a fancy machine to determine if my DNA primers are working to make lots of copies of the DNA from my plant seedlings.

In a different part of the lab, I took some of my seeds already set out on agar plates from a refrigerator where they were experiencing simulated winter and moved them to an incubator where they are now experiencing simulated spring. I’ll later get all of their DNA too. And in still another part of the lab, I continued to work with something called “primers” which are used to help make many copies of small quantities of DNA. I know what you must be thinking: “Just how big is this lab?” Luckily, pretty big!

I weigh the dried plant tissue to determine how "weedy" my different treatments are.

I weigh the dried plant tissue to determine how “weedy” my different treatments are.

Aside from the writing and lab work, this month I also got to be in a research-related mini photoshoot of sorts. Remember that children’s activity book about green roofs that I wrote and published last year? Well, the Chicago Botanic Garden is going to be featuring the book in a small article published in their quarterly magazine. I got to feel like a celebrity for a few minutes while I got my picture taken for the article. Of course I’ll share the article on the blog when it comes out – maybe as soon as next month!

Smile! I had fun participating in a mini photo-shoot related to my green roof activity book.

Smile! I had fun participating in a mini photo-shoot related to my green roof activity book.

And finally, in case you’re interested in the more technical side of some of the research I’ve worked on in the past, my “Publications” page has been updated with downloadable full text versions of many of my research papers.

Happy New Year!

Research update: September 2015

It’s fall once again in Chicago and you can really begin to tell on the green roofs. They’re still looking good, but most of the plants are starting to turn brown, shed their seeds and get ready for their long, cold winter up on the rooftops. It almost getting too chilly for this roof top botanist to enjoy collecting data outdoors so it’s a good thing that the work is starting to gradually move indoors.

It's fall on the green roofs. The plants aren't dead, they're just beginning to go dormant for the winter.

It’s fall on the green roofs. The plants aren’t dead, they’re just beginning to go dormant for the winter.

To start off the month, I spent a weekend in Michigan with the other Northwestern University Presidential Fellows. This group of outstanding grad students from a wide variety of departments in the graduate school is doing some amazing research! As one of the fellows, I got to share my research with the others in a relatively informal presentation. I really liked learning about what other graduate researchers are doing and I loved getting to answer some difficult questions about the motivations behind my own work. I’m looking forward to more presentations with this group in the future during my next 2 years as a fellow.

In a more formal setting, I also shared some aspect of my ecological research through a new course I’m teaching. Twice a week, 45 undergraduate students at Loyola University and I learn together about the environmental issues that impact us and the world we live in. As a former high school teacher and undergraduate instructor, this is something that I really enjoy doing! I get to teach the students a little bit about the ecological benefits of green roofs but also learn about some of the bigger picture concepts, like the importance of water conservation, right along with them. With a motivated and enthusiastic group of students, it’s looking to be a pretty good semester!

As I take a last look at my green roof plots this fall, I make a note of any new growth. This little native cactus started off with just one pad (the one on the left) and now it has two. Good luck over the winter little guy!

As I take a last look at my green roof plots this fall, I make a note of any new growth. This little native cactus started off with just one pad (the one on the left) and now it has two. Good luck over the winter little guy!

In terms of research, I started to conduct my last “checkups” on the green roofs. These checkups involve collecting data from the temperature probes that I have buried there and resetting the probes to collect data all throughout the winter. I also collect all remaining weeds from the green roof trays so I can clean, dry, and weigh them back at the lab over the winter. I fix anything that’s broken and make any final notes about the plants. After the final checkups at my 5 research sites, I won’t be back until April or May. So I cross my fingers that all the plants and probes are still there when I come back in the spring.

As the outdoor work winds down, the indoor lab work and writing start to take up more of my time. I’m now working on figuring out a new procedure for getting as much DNA as possible out of the tiny little seedlings that I was growing in the spring. In September I tried two new procedures and unfortunately neither of them really worked. So now it’s time to try procedure #3 – hopefully I’ll have some good successes to report in next month’s research update. Wish me (and the little seedlings) luck!

Small tubes full of plant tissue heat up as I try to develop new methods for getting DNA out of tiny little seedlings.

Small tubes full of plant tissue heat up as I try to develop new methods for getting DNA out of tiny little seedlings.

Research update: August 2015

Once again, August was a busy month, filled with field work, lab work and even a conference! It’s fun to look back and see what I was able to accomplish.

One lonely pinnate prairie coneflower blooms in my green roof prairie plot. It's trying to attract some pollinators - go little coneflower, go!

One lonely pinnate prairie coneflower blooms in my green roof prairie plot. It’s trying to attract some pollinators – go little coneflower, go!

The month started with completion of the vegetation surveys that I was conducting on 3 of the green roofs in the Chicago area. These vegetation surveys allow me to measure the height, coverage and reproduction ability of the various plants that I planted on the green roof. With the rainy summer we’ve been having in Chicago, most of the plants are doing quite well and my little plots continue to look like mini-prairies. Originally, August was supposed to be the last time that I had to take these measurements. But my mini-prairies are looking so good (and I’m such a botanist!) that I want to come back next year and measure them again. We’ll see if that’s still the plan come 2016.

Funny hat? Socks hiked up over my pant legs? It must be time for data collection in the prairie!

Funny hat? Socks hiked up over my pant legs? It must be time for data collection in the prairie!

Speaking of prairies, I also visited an actual prairie for my research (on the ground this time, as opposed to a rooftop). Two interns from the Chicago Botanic Garden and I took a trip to a large prairie in central Illinois to collect leaf tissue from the same species of plant that I’m studying on the roofs. I am looking at how pollen movement in this species can help increase the genetic diversity of green roof populations. But I wanted to know what the genetic diversity of this species is like in natural populations, in real prairies. So we collected leaf tissue from a natural population, extracted the DNA from the leaf cells, and are now working in the lab to measure the diversity. This is a work in progress, so stay tuned for the results. If anything, it was neat to see the plant species I’m working with in its natural habitat.

Interns from the Chicago Botanic Garden help me collect leaf samples from the natural prairie population.

Interns from the Chicago Botanic Garden help me collect leaf samples from the natural prairie population.

In addition to collecting lots of data, I was also fortunate to be asked to present some of the overall findings of my research so far. I’m still working on collecting some more data from internet sources and analyzing my results but I am beginning to find some trends with the data that I collected back on the green roofs in Germany in 2013. It seems like there are very few patterns that predict which plant species colonize green roofs and survive on them over time. It looks like each green roof is a unique place with its own community of plants and animals that live there. I was able to share these results (and others) at a special green roof session of the Ecological Society of America’s annual meeting in Baltimore, MD. And not only did I get to present my research, but I got to attend lectures and workshops where I learned about other people’s research too. It was a busy week in Baltimore and even though I came back tired, I was also inspired and excited to keep making discoveries with my own research.

The hotel at the Baltimore Convention Center had a green roof. A great inspiration view as I prepared to give a presentation about my green roof research at the ESA conference.

The hotel at the Baltimore Convention Center had a green roof. A great inspiration view as I prepared to give a presentation about my green roof research at the ESA conference.

And finally, in August I started to work in the lab again to continue work that I’ve been doing for about a year now. The lab was super busy with summer interns but toward the end of the month things quieted down a bit and I could claim some work space back. I’m ready to continue the work I was doing back in the spring. It’s time to find out if I can determine the father plants of all the seeds that I collected last fall and grew up into little seedlings over the winter. It’s going to be a lot of work but I’m looking forward to being a bit of a botanical detective!