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Here at the Echinacea Project, we have some pretty rigorous protocols to make sure that everything goes right. This applies doubly so when it comes to ACE — the process we use to make sure we count all of the achenes on every head (hence the acronym, Accurately Count Everything). The process starts when we harvest the head in Minnesota in August or September, and ends sometimes years later when we have classified the last xray, with rigidly defined steps in between. This process leads us to a data set that has a human error rate of less than 1%
This is a story about that <1%
In fact, I would argue that this is a story about the 1% of that <1%. A head that has not only 1 terminal error associated with it, but 3.
This is the story of CG2016 XD-9460.
My experience with this head, whom we’ll nickname XD, began when Tracie gave me a list of the necessary rescans for 2016. These are the heads that, for some reason, never had their achenes scanned. They can be particularly troublesome because usually their achenes are in 3 separate places as part of ACE protocol that normally comes after the scanning step. I had gotten XD’s achenes from 2 of the 3 locations, and went to look for its orange coin envelope — the envelope that contains most of its achenes.
It wasn’t in the first place I looked, where it should be.
It wasn’t in the second place, where it shouldn’t be.
Nor was it in the third, fourth, or fifth places I looked, where it definitely shouldn’t be.
In fact, it was no where I looked. After an upsettingly long and painfully fruitless searching process, I decided to check and see who had cleaned XD, and maybe that would give me a clue where the envelope was. To my surprise, I saw the label that should have been on XD’s orange envelope still on the master label sheet, and the words “head not here” written in the notes section by the volunteer assigned to clean it.
How then, did we have some achenes for XD if the head was never cleaned? How did we have achenes if the head was never here?
This is an insight into our ACE protocol. Even with our organization and attention to detail, things can go wrong in ways we could never predict. After I completed my detective work, here is what I believe happened to CG2016 XD-9460. This is the verbatim note I have left in our “missing scans” log. It is unusual for this log to contain more than 10 words about each head.
1:56 12/5/2018 MCL
XD-9460 has more than one error associated with it. This is my best guess as to what happened.
Error 1. On the day it was harvested, the harvester came to a plant that had two heads on the ground: XD-9460 and XM-9011. The harvester put both heads in the same bag and made a note of it. I believe that bag was labelled XM-9011
Error 2. When it came to cleaning, XM-9011 was cleaned normally, and no note of a second head was ever made. I believe only one head was selected from the bag (either 9460 or 9011), labelled as XM-9011, and processed, while the other was ignored.
Error 3. During randomizing 9460 was not skipped, despite having no seed packet associated with it There is a white envelope and clear baggie with achenes “from XD-9460” in it; however, seeing as that is not possible, they come from a completely unknown source.
So there you have it. A story that took up a few hours of my time, so I thank you for taking a few minutes of your time to read it. If you’re wondering what happened to the data from this head, it has been labelled as “lost in the field” and wont poorly influence our analyses (or torture our lab managers) anymore.
Have a good weekend!
Michael
Hi flog,
Things have really gotten going, here at Echinacea headquarters. Julie, Sarah, Lea, and I have been spending much of our time cleaning and counting Solidago, and we’ve made pretty good headway, each counting about 2-3 samples per hour. We’ve also made some preliminary observations about variability. We’ve found high variability between plants, but not within plants! For example, we’ve seen ranges of 3 to 372 heads per stalk, and anything from 7 to 24 achenes per head in different plants. But within a plant, achenes per head is relatively uniform, generally ranging by ~2 achenes, which should allow Lea to precisely estimate total number of achenes per plant.
In addition to the Solidago, we’ve been working on Liatris. We finished the most important part of estimating potential reproductive success: x-raying the achenes to see if they contain seeds. This process involves placing baggies filled with Liatris achenes over a reusable x-ray film, shooting x-rays through the achenes, and quickly feeding the film through a machine that digitizes the film and allows for online counting of full and empty achenes. From this, we can estimate proportion of achenes containing seeds, multiply this proportion by number of achenes, and thus estimate reproductive potential of the plant. Because my project doesn’t involve seed set, Julie will be doing all the counting for Liatris (Fig. 1) while Sarah will handle counting for Solidago x-rays.
Until next time,
Tris
Fig. 1. Julie diligently counts full and empty Liatris achenes while Lea continues to count Solidago heads.
Hi Flog!
With half of our externship now past, some exciting things are happening in the lab! Yesterday, Sarah, Tris, and I had the opportunity to talk with Stuart, Michael, and Lea about some of the research questions and hypotheses we’ve started to form while working so closely with the specimens over the past week and a half. Stuart offered several suggestions about how to formulate these questions so that they are testable with the kinds of data we have, while also advising us about the statistical approaches we could take to assess our hypotheses. As we gather together the last crucial pieces of data, we’ll have the opportunity to try answering some of these questions. If all goes well, we will be rounding out our experience working with Team Echinacea by the end of next week with our own independent projects and analyses of the data.
In the meantime, we have been continuing our final steps of data collection. Despite our earlier trials and tribulations holding our breath while individually counting hundreds of seeds the size of sand grains, our new Solidago counting procedure seems to be a success! With a more efficient system in place, we hope to finish counting seeds by the start of next week. All that remains after that is x-raying and classifying the x-rays from all of our samples of Echinacea, Liatris, and Solidago before we can gather together all of our data into frames. As we learn more and more from our mentors about how to manipulate data sets in RStudio, I can’t wait to start assessing regressions and comparing models soon!
Excited for the number crunching,
Julie
Tris and Sarah demonstrating our new and improved Solidago counting procedure
Hi Flog!
As we near the halfway point of our externship with Team Echinacea, it’s time for a progress update! Julie, Tris and I have been knee-deep in data collection for the past week and a half: this includes both the “ACE” protocol with Echinacea achenes (cleaning, re-checking, scanning, counting, randomizing to create X-ray samples) and similar processing with Liatris and Solidago specimens. We quickly learned that the pappuses (papi? – the fluffy bits designed for wind dispersal) of Liatris and Solidago achenes adds a new level of difficulty to the counting and randomizing processes. Any air movement–including breaths–can cause major disruption to our work spaces, and the achenes themselves are often frustratingly small.
Though we finally made it through the Liatris samples by the end of last week, with this week commenced the Great Solidago Counting Problem of 2018. With minuscule achenes, of which there may be many hundreds on any given sample, Solidago is not easy to work with–especially when you’d like to estimate achene count per plant. We spent much of our afternoon workshopping several methods of estimation and randomization with Lea and Stuart, hoping to make the process as efficient as possible while also providing reasonably accurate achene counts for Lea to use in her ultimate data analysis. Our final method (still subject to change and optimization) consists of counting the number of heads on each sample, then randomly selecting five heads from which to count achenes. This way, we can extrapolate average achene count per head to the number of heads, then to the number of total florescences of the plant. We hope to power through the remainder of the Solidago samples within the next few days, then begin analysis of all the data we’ve collected!
Until then,
Sarah
Julie, happy to randomize some Echinacea rather than count Solidago
Hey, my name is Leah Rose and I am an intern from Lake Forest College! During the last few weeks, I have been working with Stuart Wagenius and Michael LaScaleia to research pollen limitation in Echinacea angustifolia to see if there is an effect on lifetime fitness when the flowers are loaded up with pollen and when they don’t get any pollen. I have loved getting a hands-on experience with researching these important native plants and helping make an impact on conservation of our native prairies! As a future high school biology teacher, experiencing science and conducting research is very important to me and I want to show my students that they can be a part of research such as this in the future. Science is for everyone and introduces you to people and subjects outside the usual scope of our lives!
Here is a picture of me totally beating Emma’s achene count! #winning
Hello Flog!
My name is Julie Bailard, and I am a junior biology major and cognitive science minor from Carleton College. I am working with Stuart Wagenius and Michael LaScaleia on their project examining the effects of pollen limitation on Echinacea angustifolia‘s survival and reproductive success. I have also been collecting data for Lea Richardson’s research determining whether the Echinacea Project’s findings apply to other flowering prairie plants with similar methods of seed formation. Over the course of my first week in the lab, I have been cleaning, counting, and randomizing samples of achenes from Echinacea and Liatris aspera. As an aspiring population ecologist, I am thoroughly enjoying this opportunity to work with specimens up close and to follow these achenes from the flower head to the data sheet. I can’t wait to start analyzing the data soon!
Outside of the lab, I enjoy reading, knitting, playing quidditch, and practicing clarinet.
Hello! My name is Sarah Allaben, and I’m a sophomore from Carleton College. I’m excited to be working with Team Echinacea for three weeks as part of Carleton’s winter break externship program. Along with Tris and Julie, I have been cleaning and processing many, many Echinacea angustifolia and Liatris aspera heads in support of projects examining the extent of pollen limitation of Echinacea and the effects of spatial and temporal factors on Liatris and Solidago fitness. However repetitive it may be, I find this process is strangely satisfying (though I do look forward to switching it up a little bit next week and hopefully analyzing some data).
Especially because I’m not quite sure what I’d like to pursue after graduating, this experience is hugely valuable for developing a better understanding of careers in biological research (and receiving advice from accomplished scientists and grad students!). I have yet to delve into too many biology classes, but I’ve found myself most interested so far in paleontology, especially in that it allows for extrapolation of past evolutionary and climatic changes to predict future outcomes of anthropogenic climate change. Yet, after learning more about Carleton’s restored tallgrass prairies, working in the campus greenhouse, and now spending time with Team Echinacea, I’ve developed a strong interest in ecology and plant biology as well! The plan is to gain as much experience in these different fields as I can over the next few years, and see where it takes me. In the meantime, I enjoy rock climbing, art, hiking, and dogs; I’m also a cross country and track runner and love trail running. I’m grateful and excited for the opportunity to work with Team Echinacea, and look forward to my next two weeks here!
Dear flog,
My name is Tris Dodge and I am a winter research extern for the Echinacea Project. I am a senior biology major at Carleton College, interested in understanding how human-driven environmental change is affecting species interactions and causing rapid evolution. I spent the summer of 2017 in Carleton’s restored tallgrass prairies, researching how herbivore exclusion affects soil nutrients and community composition. Last summer, I was a research assistant for two projects at the Rocky Mountain Biological Laboratory (RMBL). I helped gather data on how changing phenology alters the competitive landscape and fitness of perennial wildflowers, and I monitored functional traits, fitness, and glucosinolate chemistry of Boechera stricta in a common garden, as part of a larger genome-wide association study. After graduating from Carleton, I hope to pursue a PhD in ecology or evolution. I enjoy spending my time outdoors and am a member of the cross country and track teams. In my free time, I hike, fly-fish, and knit.
This winter, I am a research extern assisting with projects testing pollen limitation in Echinacea angustifolia and how isolation in space and time affect fitness of Liatris aspera and Solidago speciosa. In practice, each day involves hours of cleaning and counting seeds while thinking about biology. So far, seed counting has allowed me to closely observe the beauty of flower physiology, and has also made me crave sunflower seeds (another Asteraceae). I am very excited to contribute to team Echinacea for these next few weeks!
Hello Flog,
As we wrap up these short few days before Thanksgiving in the lab I would like to share with you some of the very behind the scenes data management we do here at the Echinacea Project. For the last few weeks, we have been working on revamping our workflow for how we add GPS points into our 24-year dataset. Ultimately, this was our result:
 How we take the data on the GPS (the bubble on the left) and get it into all the different formats we need Well maybe this isn’t exactly “light” reading, but it does offer an insight to just how many steps there are to managing this data.
Hope you all have a wonderful Thanksgiving!
Michael
Hello! My name is Emma Carlson, and I am one of the Lake Forest College student interns working at the CBG! I am currently working with Tracie Hayes and Stuart Wagenius on the aphid exclusion and addition project. Over the past few weeks, I have been working on cleaning Echinacea heads, as well as randomizing and counting achenes! I have thoroughly enjoyed being a part of this project and being able to actually DO science! As a future science teacher, I always want to emphasize to my students that science is not just something you learn or read about, but something that you do and engage in! Science is about exploration, discovery, research, and hands-on problem solving. I am LOVING this opportunity to get out of the classroom and actually do science with this internship!
I am so thankful for this opportunity to see and experience how all of the different parts of the project, such as counting thousands of achenes, contributes to the overall importance of the study. This mini-internship has been an extremely valuable experience for me, and something that I am honored to be a part of!
Here is a few photos of me, working super diligently to beat Leah’s overall achene count for the day!
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