Developing a class to show the usefulness of phylogeny in taxonomy
Danny
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@Anthony came to our last scheduled community meeting and brought up the possibility of doing a crowd-funding campaign to raise capital to run the lab. In talking about that idea I pitched that a workshop for the communities he knows best would be something worthwhile to deveop. Ellen mentioned the taxonomy issues in mycology.
Today I saw this video and it reminded me of the types of theoretical lessons we could teach at this workshop (for fungi instead of animals) and couple with the process of sample prep, PCR, sequencing and tree making
Starting this thread to get a sense of what would make this interesting to the most amount of people and who would like to help with such an endeavour.
Poll Created Thu 16 Mar 2023 8:41PM
Forming a small crew to work on creating this workshop and delivering sometime in Summer 2023 Closed Tue 28 Mar 2023 3:04PM
Alright we got some folks responding so I'll make a poll to set up a time to meet. It's not clear to me that some of the "yes" respondents are aware of the crew mentality based on the responses but we can talk about it in the first meeting! Thank-you as well to those who responded with a "no" it's nice to see some life on a thread that's been inactive for some time.
As I think about the year ahead I'm looking to bring old threads to a close so that we can collectively focus on new things. Although the results of the last poll on this thread are from 2021 there was a reasonable amount of people who participated. In re-reading the context of the thread I am able to reconnect with my enthusiasm for the potential class. (I also have learned a lot about Loomio and organizing within Biotech Without Borders since then and am eager to apply myself)
Thus in the spirit of microsolidarity and spring cleaning I'm looking to form a small crew to develop this class. Folks can see first-hand how I have approached classes in the past and we will aim to have this developed and scheduled for delivery in Summer of 2023. I'm also eager to learn from others about their pedagogy and thoughts around the utility of methods used to generate this phylogenetic data.
In addition to the scientific curiosity being satisfied this will be a mechanism to raise funds for Biotech Without Borders, but I intended to ensure course materials are freely available as I have done in the past. In fact, part of the class is done already as I collaborated with Craig some time ago to add these slides to excerpts from one of his decks.
If you're willing to join a small crew (no more than 6, ideally 4, the linked resource is from Enspiral and they call them pods, although there are many links on the microsolidarity crewing page to other potential models) to develop this class please let me know in the poll. I'm willing to work with some folks remotely, but ideally there will be at least 1-2 folks who can meet in person. This will require at minimum a commitment to create a deliver this class in the summer, but I'm open to other shared commitments as well.
Results
| Results | Option | % of target | Voters | |||
|---|---|---|---|---|---|---|
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Accept | 133% | 4 |
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| Decline | 3 |
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Undecided | 59 |
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7 of 66 people have participated (10%)
Anonymous Wed 1 Dec 2021 3:17AM
| 3 - Assay pet stool samples | ||
| 4 - Pet dog genotyping | ||
| 5 - Cannabis related | ||
| 6 - Cheese fungal related |
I think it is a natural step toward human assay and genotyping. Useful and valuable to set up the means of obtaining this data in pets with aims later to be able to move on to humans, if feasible.
Poll Created Wed 1 Dec 2021 3:16AM
Which potential workshop are you most interested in? Closed Tue 7 Dec 2021 1:02AM
Looks like we had an OK turnout of voters. I also think this anonymous voting function is a nice way to not have any strong personalities dominate the results. However, it also means that we lose observations on those who are engaging regularly. It signals to me that we might have to do some sort of regular (but infrequent) check up on folks and remove them from the Loomio if they are very inactive.
Anyways, the phylogenetic mysteries class rose to the top, but there is interest in all the workshops including some that were added to the list. We'll probably get around to them eventually (and if you want to discuss or develop those ideas further please see the context bar at the side of this thread).
I also see a comment about pet genotyping/stool assays as a pathway to human genotyping/stool samples. I don't think that we need to do a stepping stone. My thought is that if folks want to test themselves more than their pets we should troubleshoot protocols for humans. Of course, we have to be careful to not provide any medical claims around these sorts of DIY tests and the biosafety concerns of human samples are elevated. If there are reasons for thinking pets before humans please let us know.
In the interest of not taking on too much new programming amidst plans for our grand re-opening, I will look into figuring out what we need for the phylogenetic mysteries class focusing on fungal taxonomy. The next steps I see moving forward are connecting with some experts in this area and troubleshooting some of the lab techniques. If you have any constructive thoughts along those lines please put them in the comments.
After combing through this thread a little more I think we're at a stage were we should get some more opinions.
So assuming an in-person course with a remote computational component please rank the options (add your own if you want but realize that too many options might be a onerous re-rank) based on which you would most likely want to see come to fruition
Results
| Results | Option | Rank | % of points | Points | Mean | ||
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Phylogenetic mysteries in fungal taxonomy | 1 | 20.9% | 23 | 2.9 | ||
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Pet dog genotyping | 2 | 19.1% | 21 | 2.6 | ||
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Cannabis related | 3 | 18.2% | 20 | 2.9 | ||
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Cheese fungal related | 4 | 17.3% | 19 | 2.1 | ||
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Kombucha related | 5 | 12.7% | 14 | 2.3 | ||
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Assay pet stool samples | 6 | 11.8% | 13 | 2.2 | ||
| Undecided | 0% | 0 | 0 |
10 of 29 people have participated (34%)
Deleted account Sun 4 Jul 2021 5:00PM
after teaching taxonomy for the first time this year to UG, i think it would be valuable to give a more equitable presentation to achieve a more exoteric basis for use. The naming and classification is archaic and lacks meaningful awareness to involve underrepresented communities. It turns into a rabbit hole that maintains dominant practices. There is a lot of room in the space for growth.
Yuriy Fazylov Fri 17 Mar 2023 8:48AM
More on the cannabis topic. I found out growers send out their leaf samples not to grow the wrong gender of cannabis. So they do DNA sex-typing and get rid of male plants, meaning there's an avenue to become a middleman for that testing for sex/gender selection. To increase numbers, they then clone the female plants.
Since every household is allowed 6 plants per person, and you can't drive, take the train, walk the streets without getting a heavy saturation of it in the air that could translate into lot of testing on cite with an ad slogan, Don't grow the wrong plant.
I don't know how seed distributors can know, but some are guaranteeing female only seeds. Maybe these are seeds of polyploids.
By the way, https://en.wikipedia.org/wiki/Radula_marginata , a liverwort produces cannabinoids. How about carrying its production into the Open Plant Project?
Deleted account Fri 27 Aug 2021 2:30PM
馃憤
Yuriy Fazylov Fri 27 Aug 2021 12:34AM
I found out that cannabis got legalized. What do you think about shaping a course around that topic instead of fungus? Growers will come. Not a lot of states can get their hands on this course material yet, creating a niche. How about it?
https://flowerhire.com/a-bumper-crop-of-cannabis-classes/ NYBG is doing it.
Danny Thu 8 Jul 2021 11:31PM
Oh man, my partner has been somewhat interested in watching these videos and I have come to the realization that because they are being actively released they represent a type of targeting we can do
Yuriy Fazylov Fri 9 Jul 2021 7:49PM
on the other hand too many primer sets in one rxn tube could be disaster
Danny 路 Wed 1 Dec 2021 3:06AM
Moving this comment out of context because I think it speaks to the context if the overall thread more than where it lay. What do you mean my exoteric in this comment?
I agree that there are naming practices that reinforce a specific historical outlook on diversity and ignores or disparages indigenous knowledge. Doing some research appropriately into the collected knowledge of different cultures and recognizing how limited our current knowledge might be, will of course be important.
It might also be why speaking about Operational Taxonomic Units would be a powerful concept in a proposed class looking at taxonomic issues in mycology (unless I'm missing the mark here; I'm not super savvy with fungi).