Talk on Sequencing and Microbes ...

I recently gave a talk where I combined what are normally two distinct topics - the Evolution of DNA Sequencing, and the use of Sequencing to Study Microbial Diversity.  Here are the slides from the talk:

My Ode to Yolo Bypass

Gave my 1st ever talk about Yolo Bypass and my 1st ever talk about Nature Photography. Here it is ... 

 

Four years - 1461 straight days - of iNaturalist observations

Well, today is a big day I guess. I just posted an observation to iNaturalist of a hummingbird in my backyard.

https://www.inaturalist.org/observations/195397005

Not that big a deal unless you are living in some place where it is really cold and you are jealous we have hummingbirds in our yard in Davis, California on December 31.

But the context here is important.

This entry completes a somewhat crazy run.  I have made iNaturalist observations every day for the last four years.  That is, every day for the last 1461 days. 

It all started in January 2020.  Before the pandemic reared its ugly head. I decided it might be fun to try and be more regular about iNaturalist postings.  I had gotten into posting my observations there during 2018 and 2019 and then I saw on Twitter some people referring to an iNaturalist "Streak Finder" where you could look up how many days in a row someone posted observations.  

And many people were discussing how many they had. And my max # at the time was OK (max of 16) but not particularly high. 

And then I kind of forgot about it. But I was inspired by conversations with Laci Gerhart and I decided I would try to do an entry every day for all of 2020.

https://twitter.com/phylogenomics/status/1214614081329487872

And things of course got complicated quickly. First major complication -- I got called for Jury Duty and was selected as an alternate for a pretty serious case that in the end ended up lasting 3-4 weeks. 

And I was pretty proud when I got through month 1 - January 2020.  I posted a thread on Twitter about this.

I also posted this on my blog here.

One of the reasons I started doing this attempt to post every day was that I was hoping to go on a lot of work trips and to post every day on those trips and this would give me something to do while on the road. 

In February I went to the AAAS Meeting in Seattle and on breaks wandered around and took pics and made lots of postings.  Plus I got to hang out with an old friend, Carl Bergstrom, and we wandered around one day looking for birds 

And things seemed good.  Except for one thing.  While at AAAS, I decided to avoid indoor crowded places because of the growing reports that this new respiratory disease had shown up in the US.  And, well, this would be my last trip involving planes until a few weeks ago.  So much for my plan to use iNaturalist as a way to help me not sit in hotels / conference centers while on trips. 

And there were many many struggles in life generally for me and many others as the pandemic spread. But somehow through this I managed to keep making observations.  In fact, I would say without a doubt the mission to make observations helps keep me semi sane during some dark times. 

And then I found myself on 12/31/2020.  I had done it. One whole year of daily observations.

https://twitter.com/phylogenomics/status/1344873226464161792

And of course lots more happened over the next year.  But I made it to 12/31/2021 and had made observations for another whole year.

And fast forward to today.  I have made it to four years of daily observations. 1461 days.  Through health issues. And the ongoing pandemic.  And all sorts of complications.  One thing that helped me in life was my mission to make some sort of nature observation I could post every day.

See https://www.inaturalist.org/observations?d1=2020-01-01&place_id=any&subview=table&user_id=phylogenomics&verifiable=any for the collection of my observations over four years.

Some 800+ species.  Some 45,000 observations. Mostly birds sure but some other things too.

Here are the most reported species during my four years:

I am incredibly grateful to all the people who helped identify my postings including those below:

And, well, I also now have a really cool record of nature observations over the last four years.  

Finally, I am grateful to iNaturalist for the system they have created. And that is why I just made a donation to them and I encourage others to do so too.

Notes on My Meningioma and Gamma Knife Treatment

So - on 9/27 I had Gamma Knife treatment at UC Davis for a posterior fossa meningioma that was first found by MRI about 6 years ago.  I am going to be collecting my various posts here on the saga. I am also going to post separate posts here about the saga but just wanted to collect some of the other posts for now.

---

Day 20. October 17.

Really brief updates. 

Had some horrible headaches last week but as of a few days ago these have lessened. No significant fatigue or brain fog so that is good.

Also - I decided to test my ability to fly on Friday and flew into a concrete pillar at a gas station and smashed my shoulder quite badly.  Fortunately it was not broken but it still hurts like hell a few days later and have not slept very well since then.  The good news is, this got me to forget about the Gamma Knife treatment ... 

Day 13. October 10. 

This was definitely a bad day. Went in to work in the AM thinking I might be able to work for their day.

First went for a really brief walk at the UC Davis Riparian Preserve. That was nice. 

Then went to my office in the Genome Center. Saw some colleagues which was nice and chatted for a bit.  Then hit by unbearable headache where my head felt like someone took 1000 big rubber bands and wrapped them tightly around my head. 

 So I went home.  Took ibuprofen which did not help.  Napped a bit.  But nothing helped. Took a bath.  Did not help. And that is how the rest of the day went.  

Sanger DNA sequencing services

 Sanger DNA Sequencing Services

So I posted a request to multiple social media sites:

Question - are there good / cheap services out there to do Sanger sequencing (e.g., for 16S / ITS for taxonomic identification of cultures)? The local Sanger operation we were using shut down.

I posted to the following sites:

• Facebook

• LinkedIn 

• Twitter

• Blue Sky

• Mastodon

These are the places that were recommended the most

• GENEWIZ from Azenta

• UC Berkeley

• Quintara

• Eurofins

• McLab

These had single suggestions

• Macrogene 
• MR DNA 
• Integrated Genomics 
• Functional Bio 
• U Az. 
• CosmosID
• Laragen
• Retrogen
• IMR
• Functional Biosciences

These are how the suggestions mapped to the different sites: 

• Facebook
• Eurofins
• McLab in south SF 
• QB3 
• Macrogene 
• MR DNA
• Laragen
• Retrogen
• IMR
• Functional Biosciences
• LinkedIn 
• GENEWIZ from Azenta
• Integrated Genomics 
• Twitter
• Eurofins
• Quintara
• Functional Bio 
• Gene Wiz (now Azenta)
• UC Berkeley
• U Az.
• Blue Sky
• Azenta (used to be Genewiz)
• CosmosID
• Mastodon
• McLab
• Quintara

And today in one of the stranger uses of my work ... "130 Academic Words Ref from "Jonathan Eisen: Meet your microbes | TED Talk""

Well, this is certainly a bit wacky.

I was, well, Googling myself today and found this.

130 Academic Words Ref from "Jonathan Eisen: Meet your microbes | TED Talk"

It seems like they took my Ted talk

and got key words from it, and then use it to teach about those words in some sort of automated way. And, well, they got a few words wrong but actually the words they chose kind of capture a lot of what my talk was about. So here are a few screenshots of some of these key words