Pushing Performance - a reflection on 2016

I started the year with a little challenge to myself based upon looking at a number of other iNaturalist users; make one observation for everyday of January. It wasn't easy, but it was rewarding as it caused me to see things I don't usually look for since in an average workday the "natural" space I may have a chance to interact with is very low.
http://www.inaturalist.org/journal/damontighe/5333-1-observation-a-day-for-1-month-my-january-2016-challenge
I wasn't able to keep the pace for the entire year, but as the year finishes out, I've some how compiled 7,000+ observations!

The challenge pushed me to be more curious about what was right around me, so I started a project on just the apartment complex I manage to see how many organisms I and maybe some of my tenants could document on this little slice of urbania.
http://www.inaturalist.org/projects/1502-alice-street-biological-monitoring
This project got me at some level to recognize the potential humans have to transform their own living areas/ecosystems as through this project I documented a fungal parasite (Entomophthora muscae) that I intentionally brought home a year previously and saw it emerge time and time again.

http://www.inaturalist.org/observations/3916249

I also sped down the slippery slope of aided observations using clip on macro lenses for my cell phone, Foldscopes, and all sorts of other microscopes, which did nothing but get me excited to no ends about all that can be found even in an urban landscape. I attempted to share that fascination with others by hosting workshops and Bioblitzs focused on the use of these tools
Here are the tools for learning to use a cell phone macro lens:
https://calnature.org/blog/2016/8/18/cell-phone-macrophotography-insects
and here are some notes from one our our Bioblitzes using Foldscopes:
https://calnature.org/blog/2016/10/17/tardigrades-and-friends-a-microbioblitz

The scientific value of iNaturalist became more and more apparent to me as the platform became not only a place for me to learn by documenting, but also a place researchers could find things I had seen and ask for them. One of my favorite interactions in this realm for the year was hunting down various forms of Laboulbeniaceae and sending them off to Harvard for @dhaelewa. An entire class of fungi I hadn't even been aware of!
http://www.inaturalist.org/observations/3830004
http://www.inaturalist.org/observations/3291539
I started using a tag "collaborationDT" so I could easily find these instances of observations that became useful for someones research.
http://www.inaturalist.org/observations?q=collaborationDT&search_on=tags

The social value of iNaturalist also became more apparent to me as I found myself on trips with people I met through iNaturalist and even one fateful afternoon I was identifying mushrooms on iNaturalist and realized @catchang and @robberfly were out exploring nearby in the East Bay Hills in real time and was able to message them and go join in the adventure. http://www.inaturalist.org/calendar/damontighe/2016/11/23
and on another occasion I was invited out to Mineral King to help researcher with a survey for mycoviruses which ended up being an epic backpacking trip
https://flic.kr/p/Mp1VYo

The educational potential of iNaturalist also became more apparent as @leptonia and I used it as part of a 1 week high school course in fungi with @lgottlieb where students surveyed a local watershed and did sequencing of fungi they found.
http://www.inaturalist.org/projects/marin-academy-2016-fungi-course
I'm looking forward to seeing the next version of this in 2017 building upon the last years lessons learned.

Partly inspired from the Marin Academy course as it gets me thinking what makes a good fungal observation I've started in the background to gear up for what I hope to launch in 2017 and call "Barcoding the Lake" which will be an attempt to make observations, collections of, and DNA Barcode organisms from Lake Merritt in Oakland, California. I've started a collection of all of the fungi that have come up this year, with relatively good images for the observations, spore prints and when time permits I'll get to imaging the microscopic features and ultimately DNA sequencing ITS for all of them.
http://www.inaturalist.org/observations?field:herbarium=Damon%20Tighe%20personal%20herbarium
After fungi I hope to move into the water and start with the mollusks, pollychaetes and eventually all of the other wonderful organisms I've been photographing there: https://flic.kr/s/aHskeL4LFD. I find the prospect of sequencing a bunch of organisms that have already been sequenced really exciting, because science is a process of repetition and for a lot of these organisms these conserved regions have only been sequenced a handful of times at best, so to get more looks at all of them on this level will hopefully be useful. Repetition is the "boring" part of science, but its what really makes it solid. Its the confirming that past experiments or observations holds true that tethers knowledge to something enduring.

I'm looking forward to all that 2017 has in store!

Publicado por damontighe damontighe, 31 de diciembre de 2016

Comentarios

Thumb

Great job! You are amazing and inspiring (to naturalists of all levels I'm sure). Just reading about everything you did made me tired....well, I was already tired and feeling ever so slightly accomplished just from catching up on uploading all my cell phone pix, ha. I always enjoy and am often mind boggled looking/reading your posts. Looking forward to more in 2017!

Publicado por flygrl67 hace más de 4 años (Marca)
Thumb

Thanks for a thought provoking wrap up for 2016! I'm new to iNat and found myself getting deeply involved as the political year gained steam. I needed an avenue to offer hope and sense of accomplishment.

So much of the utility of this site you mention above became apparent immediately. I as well became curious about the natural world's resilience in urban Oakland, especially in my neighborhood where I spend much of my time in. Also tried posting something every day (hard to do- see the white crowned and house sparrow posts!). But most importantly, I found impassioned people and researchers focused on exploring and learning about the world around us.

I was raised by my Native Hawaiian family to care for the land and all the flora and fauna. Walking around and paying attention to each plant is the way my grandmother transmitted cultural knowledge to me- how each plant can become useful, which are medicinal, which edible, etc., way before I understood taxonomic classification. So in a funny 'futuristic' way iNat is sort of natural to me. What's truly different is the way it helps build networks for research and stewardship. We need malama 'aina and science is critical in that regard as we move into climate change.

I look forward to seeing more of what work you continue in 2017. Ping again if you find me posting nearby in real time, that was super fun! Happy new year and Mohala i ka wai ka maka o ka pua, Cat

Publicado por catchang hace más de 4 años (Marca)
Thumb

@flygrl67 - so glad to have you on iNaturalist. Its really cool getting to see all the cool fungal finds you see down in the central coast.

@catchang - My post-everyday-experiment didn't result in white crowned sparrows, but there are a ton of household flies in those posts! I'll definitely ping you if I see an opportunity to join you in another adventure and will send out reminders to you when I see something Calnature.org is doing that walk that line of malama 'aina as there is much there for us all to learn. Happy New year!

Publicado por damontighe hace más de 4 años (Marca)
Thumb

How could I help if I get a secondhand sequencer? Can citizen scientists help with sequencing some of their observations?

Publicado por sarka hace más de 4 años (Marca)
Thumb

@sarka A second hand sequencer isn't needed as so many businesses now offer sequencing as a service for between $5-10 per PCR sample (amplified small segment of the genome), which does mean that what a citizen scientist really needs access to is a Thermal Cycler, pipettes, and horizontal gel box to amplify conserved regions and confirm that amplification took place. A project coming out of the University of Guelph called Life Scanner ( http://lifescanner.net/ ) also was offering ~$40 / 4 samples and all you had to do was put your organism in a vial of preserving fluid and send it in. I tried the service and got mixed results. Insects worked really well, but polychaetes and bird feather proved to be difficult. @kueda recently sent in another batch and I'm interested to hear how his results went.

Probably the easiest way to get involved generating helpful DNA sequences is first pick a taxa you are interested in working with as it will help streamline lab protocols and even analysis. Get or get access to the hardware- a thermal cycler, p20 pipette, horizontal gel box and the reagents; primers, master mix, agarose, TAE buffer and a DNA stain. There are a number of BioHacker / DIYBIO spaces popping up around the country that would have all the materials you need. See this list:
https://diybio.org/local/
If you hare looking to go the hardware route I would look at these inexpensive hardware options:
MiniPCR - http://www.minipcr.com/
BentoLab - https://www.bento.bio/

Here are my protocols for working with bacteria and with plants
https://www.dropbox.com/sh/phq3kybpfx3736x/AADH3CGlm6VJDv1sfZerueZUa?dl=0

Sequencing Services I've used before (in order of performance).
GeneWiz
Sequetech
Eurofins

If you have an idea of what organisms you'd like to try and sequence I can help get you protocols based upon what is in the literature for your taxa of interest.

Publicado por damontighe hace más de 4 años (Marca)
Thumb

This was the disappointing response I got from LifeScanner after I again had to specifically ask them for the sequences of the samples I sent in the last time:

Apologies as it seems there has been a miscommunication as I did not make things clear last time. The app was designed for citizen scientists and meant as an identification service. As such does not have sequence download or analysis abilities. We have been, as an extended service, providing users interested in the DNA Barcodes access to these through datasets on BOLD on request.

So the sequences are out there, but only several weeks after being notified of an ID, and only after I specifically emailed to ask them for the sequences. Even more disappointing, the LifeScanner app has not been updated and still only uses the date / location of when you add records. So if you collect specimens, bring them home, and then enter them into the app, they'll be associated with the location of your home, not the collection location, and you can't edit this. Thus, I have a bunch of records up on BOLD right now with inaccurate coordinates and dates that also reveal the location of my home. I do not have the power to edit these records, and they have not been changed despite my request that they be updated.

Which is a long way of saying LifeScanner seemed promising but has proven a disappointment. With a few small changes in protocol it would be cool, and with some major changes in technology (e.g. iNat integration) it would be great. It is a way to get a sequence with zero biotech expertise and some finagling, so I guess that's something.

Damon, I know I keep saying this and not doing anything about it, but I would like to help with the sequencing project if you need manual labor. I will even attend a meeting if that's what it takes!

Publicado por kueda hace más de 4 años (Marca)
Thumb

@kueda - I'm slowly gearing up to do a sequencing project that I'd like to get the public involved in for 2017 and will definitely let you know once I have all the ducks in order.

The Project - "Barcode the Lake" - I'd like to have an ongoing project where a physical collection of species from the edge and in Lake Merritt are kept. From that collection I'd like to have the public learn about molecular biology techniques such as PCR, DNA Sequencing and Bioinformatics in relation to taxanomy, its benefits and shortcomings. At present time I've started on the fungal portion of Barcode the Lake in that I've been building the collection this year since we've had all the rain. Once I have a location where I know we can run this program, hopefully the RNC Library, I'll let you know and get you involved.

Here is the collection so far:
http://www.inaturalist.org/observations?q=BarcodeTheLake&search_on=tags

Publicado por damontighe hace más de 4 años (Marca)
Thumb

I wish I lived by this lake! Cool project.

Publicado por sarka hace más de 4 años (Marca)

Agregar un comentario

Acceder o Crear una cuenta para agregar comentarios.