3D Printing Authentic Fossil Samples

I had some biology students developing a guest lesson on fossils, and we got to thinking about how we could put real fossil examples in the hands of students. Here are our standards:

Sure we can find some fossil examples on Thingiverse, but what we can find are somewhat hard to predict, their organization does not have a scientific basis, and their origin is not always clear (not to mention concerns about the company practices of the owners of the platform). I wanted to look elsewhere for better models provided by organizations more aligned with my professional values.

I found GB3D Type Fossils. Here is who they are and what they do (from their own website):

“The GB3D Type Fossils Online project, funded by JISC, aims to develop a single database of the type specimens, held in British collections, of macrofossil species and subspecies found in the UK, including links to photographs (including ‘anaglyph’ stereo pairs) and a selection of 3D digital models.”

You can search at their home page using appropriate scientific names for the samples you want to find. Check it out:

From the search results you can find actual research samples, linked to their papers and researchers. It comes with high-res photos and 3D scans of the sample.

3D scans are still pretty finicky, so you’ll want to groom the model before you go to print it. We’re going to bounce back and forth between a couple programs to get this bryozoan ready to print:

  • Meshmixer – Processing software from Autodesk, for fixing model errors and generating supports.
    • Free, but not open source.
  • Slic3r – Slicing software for converting models to 3D printer instructions.
    • Free and open source

Step 1: Make the scan a “solid” – Meshmixer

This will take the crazy scans you get from researchers and forcibly make it something slicing software can interpret.

  • “Import” the .obj that you download from GB3D and extract from the ZIP file.
  • “Transform” the model and drag it up and over so it’s positioned in the middle of your build plate.
  • “Make Solid” and let the computer fix this nonsense.
  • “Export” the model as an .stl

Step 2: Orient the model – Slic3r

This will take your (probably wonky) model and orient it for printing. You might be able to skip this step, if you don’t need to rotate your model. This example needs it, because the flat bottom is not actually aligned with the build plate.

  • “Add” your recently exported .stl of the fossil.
  • Select the fossil model, and click “Rotate to Face” (see below)
  • Click on something that should be the bottom.
    • Even apparently flat surfaces are probably not truly flat. We need to fix this, so don’t be fooled.
  • “Export STL” and you can overwrite your previous .stl with this new file.

Step 3: Perfect the bottom – Meshmixer

This will smooth the rough bottom surface, so our print will actually adhere to the build plate.

  • “Import” the recently updated .stl file of the fossil from Slic3r.
  • Use “Plane Cut” to chop off the very bottom surface (see below)
  • OPTIONAL – If your fossil requires supports, now is the time to add them.
    • Find Meshmixer supports under “Analyze” → “Overhangs”
  • “Export” the finalized model as an .stl

Step 4: Print – Slic3r (or whatever)

The model is done and you can now print using whatever your preferred printing workflow may be. Slic3r does a good job creating Gcode, and a simple extension can convert it to .x3g if your printer requires that.

Don’t forget OctoPrint – an awesome Raspberry pi printing option

From here you can go give your students fossils to analyze! I imagine asking them to paint the samples to highlight what they think they are seeing could be cool. They could also color-code homologies across multiple fossil types.

How else could you use fossils in class? Share your ideas and photos of your awesome prints!

In My Classroom: Trying to make Cellular Respiration & Photosynthesis suck less.

Hey all! While having coffee with KABT President Rhodes on this lovely Presidents’ Day, she suggested I share this activity that I did with my AP Bio students recently.

If you know me at all, then you probably know I don’t particularly care for teaching photosynthesis and cellular respiration. Yes, they are important topics, but I find them to be incredibly dull. And it shows in my classroom. This year, I started my energy unit in AP Bio by saying “This will suck, and I’m sorry, but we just gotta do it”. Bad teaching, I know.

HOWEVER, there was some exciting research that came out recently from Paul South at the U.S. Department of Agriculture. His team found a way to streamline photorespiration in tobacco plants, which increased plant growth by 40%. If I could get excited about this topic, then I figured my students might as well. I also saw the perfect opportunity to introduce scientific articles into my class and to let my students struggle with understanding primary literature.

I started by giving my students the article from Science (You can read it here: http://science.sciencemag.org/content/363/6422/eaat9077)

I used this guide from Rice to help my students understand the research and to break it down into manageable chunks. http://www.owlnet.rice.edu/~cainproj/courses/HowToReadSciArticle.pdf

After we dissected the article, we had a Socratic Seminar in class to discuss the research. It was cool to hear my students speak about statistics, evolution, GMOs, and, yes, cellular respiration/photosynthesis in a meaningful, authentic way. Socratic Seminars are new to me and they’re a tool I’m hoping to use more often. My students seem to learn a lot from each other and are engaged in the discussion. To help facilitate the discussion, I gave my students a handful of open-ended questions to discuss, such as “Why do you think Rubisco uses O2 in place of CO2 about 20% of the time? What does this suggest about the plant’s evolutionary history”, and “Why does increasing plant biomass matter to humans?”.

Anyway, that’s it! Socratic Seminars! Yay! Reading primary literature! Yay!

2019 Summer PD – Ecosystems Across Kansas (Konza Prairie)

Several universities across this great state have partnered together on a massive interdisciplinary project (MAPS – Microbiomes of Aquatic, Plant and Soil Systems). As part of this project, they are holding annual Summer Institutes for teachers interested in these fields. This summer is the second edition, being held 17-21 June 2019 at the Konza Prairie Biological Station. Participants are given travel allowances and a stipend, and anyone with a commute >1 hour driving time from Konza will be provided with lodging.

If you are interested in applying, click here.

If you have any questions, contact one of the project leaders, Dr. Peggy Schultz (pschultz@ku.edu). KABT Members Drew Ising, Michael Ralph, Marylee Ramsay, Andrew Davis and Bill Welch were participants or organizers for the first summer institute and can also help.

KABT 2018 Fall Conference

The 2018 fall professional development conference will be held at the KU Field Station’s Armitage Education Center from 9:00 AM to 5 PM on Saturday, September 22nd. There is a $15 on-site registration fee and an optional year-long KABT membership for an additional $15. Yellow Sub sandwiches will be provided for lunch. Please view the attached flier for the schedule and contact sarahettenbach@gmail.com with any additional questions.

PBL: Water Quantity and Water Quality

A *New* Biology Adventure for Your Kansas Students: PBL – Water Quantity and Water Quality
KNE NewsThe NSF Kansas EPSCoR project titled, Microbiomes of Aquatic, Plant, and Soil Systems across Kansas (MAPS), a collaboration of researchers from KU, K-State, WSU, Fort Hays State, and Haskell Indian Nations University, hosted 12 Kansas biology teachers in a 2018 Summer Institute from June 4-8, 2018. Broken into three teams — Aquatics, Terrestrial, and ArcGIS, our goal was to work with researchers to investigate how the microbiomes of Kansas are critical to understanding several key issues for our state, including agricultural sustainability, water quality, greenhouse gases, plant productivity, and soil fertility. In addition to using ArcGIS to map native and restoration prairie species distribution under the direction of Drs. Helen AlexanderPeggy Schultz, and Jim Bever, we all did some aquatics field work led by the Deputy Director of the Kansas Biological Survey, Dr. Jerry deNoyelles, and Assistant Research Professor, Dr. Ted Harris, who specializes in Harmful Algal Blooms (HABs). We learned how to use lake surveying equipment to test water quality parameters and sampled macroinverts in thermally-stratified Cross Reservoir. We also seined Mud Creek, where Drew Ising apparently stumbled into a parallel universe when I botched this pano:

KNE News

The end result was this *NEW* PBL on Water Quantity and Quality, which I hope benefits your Biology students as much as I know it will benefit mine:

KNE News

About Me and my PBL Life
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