I wanted to make it known that I updated the Repeating Crumley Setup post to include the source of the water used in the experiments. Check out that link for the info you may need.
Category Archives: Water Type Effects on Organism Growth
The Crumley Spreadsheet
Spreadsheet
If you don’t want to look at pictures of gradual change every day then you can just come back to this spreadsheet to see the numbers change and then you can look to see what days something new happened and find the corresponding images through the blog. If I remember to, I may link blog posts with activity to the day number in the spreadsheet, which would be a great idea (but like I said, if I remember).
Update: slide all the way over to the right to see links to the image notes from this notebook corresponding to that day.
Update 2: I added the original Crumley Data on a separate sheet, and I began plotting the percent germination in real time. Currently I’m not sure how to label each line in Google Spreadsheets. I can’t find a way to do it, but I’ll mention it here:
- Blue – DI water
- Red – 33% D2O
- Orange – 66% D2O
- Green – 99.9% D2O
- Purple – DDW
- Not shown – di water, no seeds
BTW: It took me a while to figure out how to do this because Google Docs changed their appearance and formatting yet again. In order to embed a Google Doc in the new format there is a “Collaborate” menu along with the usual “File, Edit, etc” menus. No longer can you go to the “Share” button and select “Publish as web page” because that button has been removed (it is not just the original share button that let’s you set documents as public and determine who you want to share with).
Repeating Crumley: Day I Part 2
These pictures are setup as in picture 1 (with a computer attached to the webcam). The webcam is a Logitech HD Pro Webcam C910 with the capability to take 10MP images and record in full 1080p.
I took one picture of each sample and then discovered that I could increase the image resolution and manually control the focus and some other properties, so I took one more (the second picture of the 66% D2O sample). From the looks of it, the image quality is more than enough for this experiment. And also between the identical pictures (with different settings) the resolution difference doesn’t make that much of a difference.
Opinions, comments, questions? Drop ’em like their hot…
Tobacco Seed Growth in Water Day 1
Here is the first of many posts of the results of this experiment (LIVE!!!).
Outside of the bubbles in the DDW sample, there is no germination almost 24 hours after initial setup.
I’m still experimenting with the setup. These images were taken with a Nikon D40 in the setup I showed yesterday. I aligned everything and put the image in focus with the aid of a webcam. I’m considering just taking pictures with the webcam and will do a trial run this afternoon. More to come…
Repeating Crumley: Day 1
As demonstrated in the setup of the previous post, I have setup 5 samples of Dark Virginia tobacco seeds with each sample being in a different water type: DI water, 33% D2O, 66% D2O, 99.9% D2O, and for poops and giggles 99.9% deuterium depleted water (DDW).
The percentages are by volume (for example 33% D2O is 2mL of D2O and 4mL of DI H2O). Each sample contains 6mL of its respective water type. I’ve determined that the volume of each cell is a little less than 7mL and 6 comfortably fits with no spillage (there is a small air bubble in the chamber). Each sample also has 30 seeds.
The sample cells were setup as follows: Seeds were counted and placed on one of four prefolded sheets of weigh paper. Airflow was a problem so I placed relatively heavy objects on the edges of the paper to prevent a seed catastrophe. After seed sorting, I prepared the water samples in centrifuge tubes for temporary holding and mixing (in the case of the 33% and 66% D2O samples). 6mL of each water type was then poured into prelabeled Analyslides. The seeds were then added with the lid of the analyslide placed on top to “seal” it. Slides were then placed on the pre-assembled photography station.
Today marks day 1 of the experiment and I am proud to report that in the 5 minutes it’s been, 0% germination is seen across all 5 samples. So far results are as expected.
Recreating Crumley: The setup (Updated)
Hi!
I’m setting up the Crumley Experiment now that I have most of what I need. I ordered some more tobacco seeds but I have no idea when those are set to arrive so I’ll begin a preliminary experiment with what I have to work out the kinks. If you are too lazy to click the link above then I’ll recall for you that the experiment involved putting tobacco seeds in different percentages of D2O and tracking seed germination.
Their setup was to put seeds in petri dishes on moist cloth. I found these slide/petri dish hybrids called Analyslide that seemed perfectly suited to this and I’m going to omit the moist cloth and instead just fully submerge the seeds. The volume of the dish portion seems pretty low (less than 5mL is my guess) and the lids create a nice seal which will hopefully keep deuterium exchange to a minimum.
I built a photography system for the dishes which works a little like an inverted microscope. The slides sit up high on some cage system rods (from Thor Labs) and the camera is mounted on a rail below aimed upward. Currently I have to use a mirror to see in the eyepiece, but I’m thinking of equipping a webcam under the camera so I can see precisely what I’m looking at.
You can see the setup below with some dummy slides and some test images. I wanted to see how easy it would be to focus on something in the Analyslide so I wrote “HI!” on a piece of paper and taped it inside. It worked pretty well.
Update: I forgot to mention where the water comes from! It is very easy to overlook that fact since water is the most used chemical in the lab. When Koch talks about setting up osmotic pressure experiments he always mentions that water is the most overlooked variable because it is everywhere and we take it’s effect on the experimental world for granted. Anyways:
All water is purchased from Sigma-Aldrich, except DI water which comes from a Thermo purifier in the lab. I purchased D2O in a 100g amount bottle product number 151882. Deuterium depleted water (DDW) is also purchased in 100g amounts and has the product number 195294.
The DI water comes from a Barnstead EasyPure RoDI filtration system from Thermo Scientific, with part number D13321. I took a picture of ours for your viewing pleasure below.
No Tardigrades in the Lightning Field
No tardigrades at the lightning field…
Well I’m not sure if that is true, but I couldn’t find any tardigrade habitats. The landscape of the Lightning Field was mostly plain (as in prairie, not ordinary). There was almost no tree or rock where I’m used to seen moss and lichen grow. It had been raining frequently so it was muddy, but I’m not in the business of bringing back dirt (and I don’t think my girlfriend would appreciate that too much either). Oh well for that…
Tardigrades in Quemado
After deciding to get some lichen and moss samples for tardigrade acquisition here in ABQ (at the Rio Grande) I decided to continue my efforts near The Lightning Field near Quemado, NM which I will be visiting for the next 24 hours. Now I have no idea what the terrain and conditions will be, but I feel like there is some chance I can find what I need.
In any case I’m going prepared. I’ve brought a few petri dishes, a razor blade (for removing samples from the wild), some latex gloves (for sterility and protection), and rubber bands (to keep the petri dishes closed). Hopefully I come back with something.
Map of Quemado, NM (You may need to zoom out)
Featured image courtesy of Wikipedia.
Field Trip: The Search for Tardigrades!
Tomorrow I plan on searching the Rio Grande Valley for Tardigrades. I found a paper yesterday by Clark W. Beasley that documents found species here in New Mexico at various altitudes. From what I read it seems like there are plenty in the ABQ altitude range and hopefully I have no problem locating them.
This is no easy feat when you consider that they are microscopic, but I have a secret. I know where they live. Apparently they like to hide out in moss and lichen so I want to collect a bunch of samples to see if I can spring them loose. There are some methods in the paper linked above that describe how to go about extraction. According to their methods, you moisten the moss/lichen for a while and then shake vigorously (I’m not joking!). After that you need to use a micropipette, for extraction and preparation for sample analysis. I don’t think I care about that and will instead focus on just bathing them in D2O from that point on.
I’m planning on collecting a bunch of samples and will probably walk along the Rio Grande Bike Trail (I figure the best chance of moss and lichen is near the only water source in ABQ) extracting samples. Of course I’m winging this, but it should be a fun adventure to say the least.
Here is the map for the access points I will most likely take:
Access Points Map If you click the link you can go to actual Google Maps and in the options select bicycling and it will show you the bike paths in ABQ. The dark green path near the access points that follows the Rio Grande is where I’ll be.
Another Update on the Tobacco Seeds
I was going to use this space to compare the two different lenses, but I was so enthralled with the quality of the one 10x lens (from Opteka) that I ended up just taking a bunch of pictures with the one lens and thought I would share it all with you.
I tried to do some reading on the subject over the weekend, but it appears there is a term called root hairs that appear during growth of the primary root (which is what the radicle turns into). Now the books I read were limited in their germination physiology but at least I now have a foothold.
I did note while taking the pictures that in every case, the DDW seeds had the most root ‘fro, then the DI water seeds, and then the tap water seeds had the least. I still think this is a product of lack of nutrients, but there may be something in the question “Why would the root fro be more prominent in deuterium depleted water than in deionized water?” They are both pure, but maybe ddw is more pure than di water? Something to investigate I think.
I encourage you to enlarge every picture up there and see the amazing resolution one attains with the Nikon D40.