My Ode to Yolo Bypass

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


 

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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.


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.





















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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.  



Day 12 - October 9

Not much to report. Felt OK muych of the day but still tired. No bvrain fog really but headaches so ... meh.

 


Day 10 - October 7 - not much to report. Not great but not terrible ...









Day 9 - October 5 






Day 8 - October 4







Day 7 - October 3, 2023. 







Day 6 - October 2, 2023.









Day 5 - October 1, 2023.





Day 4 - September 30, 2023


 



  


Day 3 - September 29, 2023 

  


Day 2 - September 28, 2023 

  


Day 1 - September 27, 2023.

Posted to many social media channels about my treatment with updates and other details and also got lots and lots and lots of support.

Here are some of the posts.



LinkedIn



Facebook







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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:


These are the places that were recommended the most


These had single suggestions


These are how the suggestions mapped to the different sites: 



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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


































































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Responses to requests for suggestions for quiet air filter for daughter’s California dorm room

 So I posted a request for suggestions on various social media sites:

"Wanted - recommendations for good / not too expensive / not too loud air filter to get my daughter for her for a small dorm room in California (and thus to filter out pathogens, allergens and smoke ...)"

I am going to compile responses here


Twitter


Mastodon

 

Facebook

 

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Summary of responses to request for examples of data sets of microbial genomes with associated phenotypic data

So last week I posted a question to many different places as follows:
Wanted - dataset(s) to test bacterial genome analysis / annotation methods. Ideally has many genomes from collection of [interesting] bacteria with associated experimental phenotypes / metadata.
On Linked In:
  • Jonathan Jacobs:"
    • All the reference genomes in the ATCC Genome Portal are freely available for non-commercial research purposes. They are also fully authenticated and traceable to physical production lots in our biorepository, and produced under ISO quality management. I’m biased, but I think we’re producing the quality microbial genomes I’ve ever seen on a regular basis - so you might want to look there. We’re producing about 100-150 new genomes every month - and many of them (about ~1/3rd) are for organisms with no preexisting genome. We have about 3,300 microbial genomes now (bacteria, viruses, fungi, protists), and all bacteria and fungi are sequenced kn both Illumina and Nanopore. Drop me an email or DM if you want to learn more or collaborate or something. Here’s a link: https://genomes.atcc.org (and here’s a link to a comparative genomics paper we published in mSpheres earlier https://journals.asm.org/doi/full/10.1128/msphere.00077-22)"
    • And then "I should also add that we have tons of metadata and I’ve hired a full time data curator to help bring metadata we have in our historical records warehouse into our digital records (ie phenotypic data from routine QA/QC testing going back to the 1920s…) "
    • Natalie Ma wrote
      • Joint Genome Institute may have this (if you're fine with an environmental microbes focus). Adam Deutschbauer has done several Tnseq libraries for the bugs and characterized their phenotypes.

On Facebook:


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Another day to think, to pause, to ponder.

Panorama of Sycamore Park and the memorial to Karim

 

A bit over 10 years ago I wrote a blog post that I repost all the time. Entitled "A day to think, to pause, to ponder" it was posted on my dad's birthday and was about the pain of him dying, by suicide, when I was in college. It was meant as a sad, melancholy post but also one about the importance of compassion and how "we can all do a little bit to improve how we treat other." When I reposted this one time a few years ago, someone asked me if I had ever met the "Compassion Guy" who frequented downtown Davis and who had a life's mission of getting people to think about compassion.  I told them, yes, indeed I had and I had talked to him on and off over the years about this topic at or near the farmer's market or at his "Compassion Corner" bench area.

And thus, a few days ago, I was devastated when I found out that "Compassion Guy", aka David Breaux, was the person whose body was found April 27 in Central Park in downtown Davis. He had been murdered. And initial reports indicated that the Police did not have any good clues as to what had happened because there were no witnesses. 

When I found out that this was David I posted a few things to social media because I wanted to make sure people knew that he was a good person, an interesting person, and was not just some random bit of information.


And I am glad I posted this because many people responded to also say that David had impacted them.

For example:


I also posted this to other places, like Facebook, and there I found out that Nat Pearson, who I had known since I was a PhD student at Stanford and he was and undergrad there, had been a first year dorm mate of David's and also had wonderful things to say about him.

I had planned to go visit "Compassion Corner" on Saturday during my regular bike outing to the Farmer's market but alas I could not since I had to go to UC Davis Medical Center for an MRI.



And then late Saturday night our town was hit again.

And soon we found out that the victim was a UC Davis student - Karim Majdi Abou Najm



And this was of course horrific. A second murder in this sleepy town of Davis. And a UC Davis student. And for me, someone who I had multiple direct and indirect connections to. Just horrific.



I decided that some NatureTherapy for me and others might be useful.



And these got some nice responses that indicated they helped some other people out there. And then in the middle of the night we got a phone call and multiple text messages telling us there was a third stabbing.



And despite a shelter in place order the suspect got away



Later we found out that the victim fortunately survived but was seriously wounded.



And all around town and at UC Davis people were justifiably both devastated and scared. So for the class I am currently teaching, we put into place every measure we could to let students NOT have to come to class in the wake of such incidents. And despite UC Davis focusing on only nighttime safety, some of us also understood that students might be afrain in the day time too (with good reason I might add).




That morning I went out for some #NatureTherapy again but this time decided to not go to too isolated a place on campus and went off campus:



I then went to "Compassion Corner" to pay tribute to David. I took some pics and posted them.



And also made a video panorama

A few other pics from the memorial












Then on May 3 there was an extended period where we heard helocopters overhead. I took some pics and found out one was from KCRA.




Turns out, they were watching overhead as police were questioning a person of interest who had been caught near Sycamore Park and was eventually broungt in to be interviewed.



Meanwhile, a fund had been set up in honor of Karim and I donated to it and suggested other do so too.



This was when I found out that Nadine Yehya, who I knew from various science communications functions and from Twitter interactions was Karim's mother.



I went back out for more #NatureTherapy for myself and to share



And I then went to the memorial for Karim in Sycamore Park and tried to get some nice pics there.



And I also did some iNaturalist observations with the goal of setting up a project in the area in honor of Karim.



And then later in the day we found out the promising news:




And important comment from Nat Pearson

I responded to it:



And also noted that I had started making iNaturalist observations there too:



And some additional details stated trickling out









And that is how we get to today.



I note - I went to see if there was anything in terms of public displays at the site of the third stabbing but did not see anything. The woman who was stabbed is Kimberlee Guillory and I would like to at some point also pay tribute in some way to her. 

At the memorials sites for David and Karim, I took a bunch of nature / landscape pics and also posted observations to iNaturalist.











Basically, I want to make sure that people do not forget Karim and David. They were wonderful people. They were taken from us too soon in a terrible way. But we can get some good out of this. And I will try my best to contribute to that.



A few other pics from the memorial to Karim












Responses to question about functional annotation of metagenomic reads


Posted a question to a few places


Humann suggestion



 







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Panoramas from the past …

In 1997, my then girlfriend (now wife) and I went camping in Death Valley. It was our fourth trip there to camp in grad. school.



I brought my Olympus OM1 and did something I thought could be cool with it. I took multiple overlapping pics of landscapes with the idea that I would use Photoshop or some such program to combine them together into large panoramic landscape images

The only problem was -- I did not know how to do that


But when I got home I got the photos developed and scanned them using a scanner I had and merged them with something like Claris Draw. Here is an example - three pics from the Sand Dunes area - and the low res panorama I made - not so bad but - well - not great either













I did the same thing in other places around Death Valley. Snapping pics and then when I got home tried to make the panoramas. This one is of Titus Canyon. Not so great but OK it reminded me of the place





Well, fortunately, I keep everything. And I got pics and slides and negatives scanned with better scanners a while back. And recently I was looking through pics and re-encountered these attempted panoramas. So with Adobe Lightroom I tried again

And, well, the results were pretty fucking nice. Here is a new stitched panorama of the dunes - probably going to get the printed and framed



And here is a remake of the Titus Canyon



I am so glad I kept my old pics in relatively good shape and got them scanned. And even though it did not work out so well at the time, I am also glad I did these "click and pan" collections now that I have better tools for merging them. This one is my favorite so far




















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