Sat 3 Jul 2021 4:16AM

Developing a class to show the usefulness of phylogeny in taxonomy

D Danny Public Seen by 50

@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.


Yuriy Fazylov
<span class="translation_missing" title="translation missing: en.poll_count_options.Accept">Accept</span>
Thu 16 Mar 2023 8:42PM

it would be interesting to see inner workings and prep for this class for another curriculum, not too distant from this, I have in mind. Plus, form follows function. I'll need to be in lab to become a part of it again.


<span class="translation_missing" title="translation missing: en.poll_count_options.Accept">Accept</span>
Thu 16 Mar 2023 8:42PM

I am pretty booked up with classes this summer as well, but will follow the group and chime in remotely as much as possible. I will be in NY a few times this year, so maybe I can plan accordingly to BWB :)


Ellen Jorgensen
<span class="translation_missing" title="translation missing: en.poll_count_options.Decline">Decline</span>
Thu 16 Mar 2023 8:42PM

I am probably going to be swamped with my own classes


Danny Fri 17 Mar 2023 1:33PM

@Blacki Migliozzi No worries Blacki. I appreciate your attention and disclosure on this thread. Hope to see you in other capacities around the lab.


Danny Fri 17 Mar 2023 1:32PM

@Eric W.Yeah it's indeed been a minute, you're still in Chicago? Happy to start a project with you Eric! Poll doesn't close until March 28th so I imagine the first meeting we'll have would be in the first week of April, but I'll use Loomio to throw some dates around when the time comes to schedule. If you know of any folks in NYC who might want to join by all means invite them.


Blacki Migliozzi
<span class="translation_missing" title="translation missing: en.poll_count_options.Decline">Decline</span>
Thu 16 Mar 2023 8:42PM

Not sure if I'll be around this summer, or if I will have the bandwidth.


Eric W.
<span class="translation_missing" title="translation missing: en.poll_count_options.Accept">Accept</span>
Thu 16 Mar 2023 8:42PM

Have experience with public events, design, classes, mycology. And it's been a minute.


Poll Created Thu 16 Mar 2023 8:41PM

Forming a small crew to work on creating this workshop and delivering sometime in Summer 2023 You have until Tue 28 Mar 2023 3:00PM to participate.

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.

Current results

Current results Option % of target Voters
Accept 133% 4 D YF EW Z
Decline 3 EJ BM E

7 of 66 people have voted (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

by Danny Wed 15 Dec 2021 5:28PM

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 Option Rank % of points Points Mean
Phylogenetic mysteries in fungal taxonomy 1 20.9% 23 2.9
Pet dog genotyping 2 19.1% 21 2.6
Cannabis related 3 18.2% 20 2.9
Cheese fungal related 4 17.3% 19 2.1
Kombucha related 5 12.7% 14 2.3
Assay pet stool samples 6 11.8% 13 2.2
Undecided 0% 0 0

10 of 29 people have voted (34%)


Danny 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).


[deactivated 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?


[deactivated account] Fri 27 Aug 2021 2:30PM



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 Thu 8 Jul 2021 11:40PM

I really like thought that a lively emeritus professor might be a good outside source. We could make a list of them and interview them for types of questions they think could be adapted into simple workshops that illustrate an important concept about biotech and are tied to specific bench skills.


Susan Harrington Tue 6 Jul 2021 4:44PM

Sure! I think that is possible.

There might be scientific complications in making these phylogenies though given the commercial interest in this product. Or maybe consumers don't know enough to demand any better (until they've purchased it and it's too late).


Yuriy Fazylov Tue 6 Jul 2021 4:04PM

About the dog idea; you mean there is potential to be price competitive and more accurate. Hand the test to a liquid handling robot protocol once 96 well plate full of samples.


Susan Harrington Tue 6 Jul 2021 12:56AM

I like this idea of community projects to solve lesser-known biological mysteries. I think most experienced scientists will have some experiments or analysis they wish would be done but are unlikely to be for some reason. I think lively emeritus professors might be a good outside source.

There is the more serious appeal for funding where you try to invent something or answer some questions of interest for a large preexisting community. But there is also the less serious side where you attempt to entertain/educate on youtube. Who wants to be a youtube science star? I am not joking about this, not that I'm volunteering. ;) But counter-culture, citizen scientists pursuing mysteries could be pretty picturesque, provided the mysteries are not too obscure. With an entertainment angle, it seems you might get a much larger audience and more money eventually if you have the stomach for it.

As for the dog idea, there are a bunch of quite pricey ($100 -$150) kits that you can get on Amazon. Judging from the reviews, people think the tests are inaccurate, and looking at some of the posted dog photos, I have to agree. And, relatively often, your dog is just classified as a 'super-mutt', which means they had nothing informative to say. We just adopted a rescue puppy, but I decided against the tests since they seemed expensive and silly.


[deactivated account] Sun 4 Jul 2021 5:03PM

could we assay pet stool in a meaningful way to provide simple bio marker trends? TOI include cAMP, microbiota, glucose, water %.


Frank Sun 4 Jul 2021 10:38PM

Actually i think both of those are within what I described, the first is people wanting to acquire a new skill for whatever reason, maybe to find a new job that requires skills they don't have. the folks in the second example are people that would be in the network of SMEs that we would contact. I'm not sure those taking a course would want to from a teacher that is teaching the course a s away to learn how to teach something.


Danny Sun 4 Jul 2021 12:44PM

Yes that is certainly how I conceptualize the programming that we offer. But I also have observed two other motivations for programming:

  • exposing topics to the public they may have otherwise not come into contact with (especially in the context of the lab bench and research) and connecting it to their experiences

  • giving folks in specialized disciplines the opportunity to teach in a different setting to develop their skills, learn from the community and promote their causes

I am familiar with the process of creating and delivering course material but less with the process of identifying folks who would be in need or interested in certain material.


Frank Sun 4 Jul 2021 1:48AM

ok. I am assuming that within BWoB competencies/services will be the ability to produce different types of courses, and workshops in response to demand . depending on the topic and course level BWoB's staff will teach courses or they tap into their network of subject matter expert volunteers to teach a class or workshop. is that roughly correct?


Danny Sat 3 Jul 2021 11:56PM

I'm not asking for anything directly. I'm trying to gauge interest in creating a workshop that caters to a specific community in anticipation of a crowdfunding campaign. We don't necessarily need our own lab space to create a workshop.

I have experience in making workshops/executing them. And it's easy for me to learn the details of a specific topic. I actually have an undergraduate course project in mind to adapt into a workshop that could speak to issues in taxonomy that could be clarified by phylogeny. @Craig Trester and I did a (IMO, under developed) class like it some time ago. That could also be a good starting point to work from.

The point is to teach people something useful that would get them interested in using a lab space and yes I do imagine that as feeding interest into some sort of crowd-funding campaign.


Frank Sat 3 Jul 2021 7:20PM

i watched the video but i'm not sure what you are asking. Are you asking how to make classes or workshops interesting to a broad audience? Are you asking that about a specific topic? is the point here that you would showcase this in a crowd funding campaign?


Yuriy Fazylov Mon 5 Jul 2021 4:37PM

People like tangible subjects. One that is near and dear to a lot them is their pet. I'd do it to mycology if it was compost, maybe wall molds, and sickly soil sample related,

Yeah, 39andmyMutt.

There is only a ton of dog lovers in tristate area (if you are doing an in person class), who'd love to find out where their dog is coming from or if pedigree of a dog holds true to the name. Another thing is that when you walk your dog and never even notice who the puppy daddy is 😆. In the dog owner world, the owner blinks and that's that.


Danny Sat 3 Jul 2021 1:18PM

WGS would need supplies we don't typically have. So I'm thinking 18S, but choosing other marker genes is an important theoretical consideration in phylogeny.

Dogs are a good idea if you know the right community for it. It makes me think about something like 23andMe but for dogs and DIY.


Yuriy Fazylov Sat 3 Jul 2021 5:36AM

so you'll do a primer led class? or WGS? I tossed Genspace an idea once. Dan did nothing with it. "people have all kinds of muts" I said. "Do dog barcoding." I think some other lab is doing that now but there is space for more than one lab doing it, I believe.