Best pics from Trip to Monterey - Day 1 - May 25, 2022

 

Went on a brief trip to Monterey, CA last week. Took lots of pics. Here are some of the better ones. Also see postings with identifications at iNaturalist.

 

Videos about using the UCSC Genome Browser for analysis of SarsCOV2

 These look pretty useful and thought I would post here. Text is from the UCSC Youtube channel

This 5-part video series is for virologists and public health researchers interested in leveraging the UCSC Genome Browser and web interface to UShER (Ultrafast Sample placement on Existing tRees). These tools are a 'one-stop shop' to understand SARS-CoV-2 through genome annotations as well as track variants by placing your samples in a phylogenetic tree with millions of other SARS-CoV-2 sequences. Use the SARS-CoV-2 Genome Browser: http://bit.ly/sarscov2browser Visit our SARS-CoV-2 Genome Browser and UShER quick start page with videos, scripts and more: http://bit.ly/ucsccovidbrowser COVID-19 Research at UCSC: https://genome.ucsc.edu/covid19.html 'The UCSC SARS-CoV-2 Genome Browser' publication: https://www.nature.com/articles/s4158... 'Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic' publication: https://www.nature.com/articles/s4158... UShER documentation, installation, source code:: https://github.com/yatisht/usher https://usher-wiki.readthedocs.io/en/... COVID-19 Genomic Epidemiology Toolkit module "Realtime Phylogenetics with UShER: https://www.cdc.gov/amd/training/covi... Learn more about the UCSC Genome Browser: http://genome.ucsc.edu https://twitter.com/genomebrowser Learn more about the UCSC Genomics Institute: https://twitter.com/ucscgenomics https://genomics.ucsc.edu/

Endosymbiosis Animations for "Biodiversity and the Tree of Life"

So I am in the midst of co-teachign a very large introductory biology course at UC Davis "BIS2C - Biodiversiy and the tree of Life". I cover much of microbial diversity in this class and also the large scale structure of the Tree of Life. 

As always, I spent a lot of time working on slides and such for this class and recently posted some animations based on these slides to Twitter and Facebook and thought I would share some of them here. For today, I am sharing the animations I made on Endosymbiosis. I posted a first version of this to Twitter last week.

Endosymbioses are so cool:

Some of the images / animations I will be using today in BIS2C at @ucdavis (I made a little movie and added music here but will have richer explanations for class) pic.twitter.com/92Eb7PMTjL

— Jonathan Eisen (@phylogenomics) April 20, 2022

Note - I added music - Mussorgsky - Night on Bald Mountain for drama ... I also posted it to Facebook:

  

And boy am I glad I did. Because multiple people commented and pointed out parts that were, well, not correct. I had lecture too soon to fix them so I told my students about this and that I would update the slides. I then spent a day updating everything and made a new version which I think is much much better.

 

OK - updated with modifications based on corrections/comments from @Sergiophyceae @mcsymbiont & @DanStarrUCDavis (note, again, these are extracted from slides with lots of other details including comments about which things don't always happen ...) pic.twitter.com/LNGO8Zs94E

— Jonathan Eisen (@phylogenomics) April 21, 2022

A good bye to my beloved Clover

 

Our adopted cat Clover is pretty sick right now and likely on her last legs. We (my family, and the family of @LoranWyman who were her previous caretakers) are very sad. I compiled some of my Tweets about her here https://t.co/JqY1Mijips

— Jonathan Eisen (@phylogenomics) April 3, 2022

Sadly, Clover is gone. I am 💔. I loved her very very very much. https://t.co/xQ1QXMQ658

— Jonathan Eisen (@phylogenomics) April 3, 2022

The ongoing saga with the UC Health Insurance Pharmacy "Benefits" Via Navitus

Well the saga continues. Here is an update.

It all started March 7. See here for a long thread and also responses.

Dear @UofCalifornia @ucdavis

This is NOT OK.

I just got a notice by letter in mail that my insurance will no longer cover the insulin I have been getting "as of January 1, 2022". Letter was dated in February and was received after March 1, 2022.

This is NOT OK.

— Jonathan Eisen (@phylogenomics) March 7, 2022

See this thread in an easier to read format here: https://threadreaderapp.com/thread/1500934973775249412.html

Well, in case you missed it. Two weeks ago I posted about the disastrous and dangerous and incompetent new University of California pharmacy benefits "system" which warned me, two months after the fact, that they were cutting off coverage of my insulin 1/n https://t.co/QuTBaQBsaQ

— Jonathan Eisen (@phylogenomics) March 22, 2022

See this thread in an easier to read format here https://threadreaderapp.com/thread/1506297722776657920.html And then I got told Navitus was going to be instructed to cover my insulins by UCOP but the message clearly was not recieved.

Well - good news for me - I have been told that Navitus has been instructed to cover the insulin I have been using. More coming soon when I get confirmation and details.

— Jonathan Eisen (@phylogenomics) March 23, 2022

And finally and thankfully today I was told my insulins would be covered.

Update - to the saga of the Navitus pharmacy "benefits" plan. I got a call today saying that my Novolog and Lantus insulin would indeed be covered by Navitus. Yay. I am very happy. Now I want to know what is going to happen to others who were harmed by the new plan ... https://t.co/yvtlODyIbz

— Jonathan Eisen (@phylogenomics) March 29, 2022

I am now interested in what is happening to others out there who have been harmed by the UC / Navitus system.

Some links to articles about Diabetes and COVID19

Posted some links to Twitter that I am compiling here too about type 1 diabetes and COVID19 with a focus on recommendations for diabetics in current COVID situation

Posting some information about #COVID19 and #type1 #diabetes that might be useful to folkshttps://t.co/q9LrTXyrAy

"Your Guide to Post-COVID Travel with Type 1 Diabetes"

— Jonathan Eisen (@phylogenomics) March 21, 2022

"As masks come off, vulnerable Americans feel left behind"https://t.co/WGDJ1eII6x

— Jonathan Eisen (@phylogenomics) March 21, 2022

COVID-19 Update: The Diabetes Connection, WHO Concerned about BA.2https://t.co/GT9xXPMNX2

— Jonathan Eisen (@phylogenomics) March 21, 2022

Coronavirus (COVID-19) – information for people living with type 1 diabeteshttps://t.co/4L8MAMGtpz

— Jonathan Eisen (@phylogenomics) March 21, 2022

Why Do Diabetics Need to be Cautious About Omicron Variant?https://t.co/IdsokhYIpO

— Jonathan Eisen (@phylogenomics) March 21, 2022

How COVID-19 Impacts People with Diabeteshttps://t.co/iOOeT6N8G9

— Jonathan Eisen (@phylogenomics) March 21, 2022

Rights for Workers with Diabetes During the Coronavirus Pandemichttps://t.co/OjGpLpWEpg

— Jonathan Eisen (@phylogenomics) March 21, 2022

This is also useful: https://t.co/gx3HDCXLpE

— Jonathan Eisen (@phylogenomics) March 23, 2022

In particular this part is important pic.twitter.com/X7EwIJyPNb

— Jonathan Eisen (@phylogenomics) March 23, 2022

This also has some useful information https://t.co/sFFkf8BtWQ

— Jonathan Eisen (@phylogenomics) March 23, 2022

For example says diabetics are at higher risk even when fully vaccinated "Garza-Silva, who is immunocompromised, and Liber, who is diabetic, are among the millions of Californians at greater risk of complications from a COVID-19 infection despite being fully vaccinated."

— Jonathan Eisen (@phylogenomics) March 23, 2022

See also

Independent risk factors of COVID-19 pneumonia in vaccinated Mexican adults

Risk Factors for Severe COVID-19 Outcomes Among Persons Aged ≥18 Years Who Completed a Primary COVID-19 Vaccination Series — 465 Health Care Facilities, United States, December 2020–October 2021

Age, Underlying Conditions Top Factors in Breakthroughs

 A Wall Street Journal analysis found that among fully vaccinated people, the ones most likely to be hospitalized with breakthrough infections of COVID-19 are the elderly and those with specific underlying medical conditions.

“In particular, people with diabetes, chronic lung disease, kidney disease and compromised immune systems were at risk of serious outcomes from breakthrough cases,” The Journal reported.

 

Lots of useful responses to question "What should high risk people do in face of relaxed masking requirements"?

 

So I posted this to Twitter.

So - hive mind. A question. If you were at high risk for COVID complications if infected, with the ending of indoor mask requirements, would you just try to avoid large indoor gatherings of people even when you wear a good mask?

— Jonathan Eisen (@phylogenomics) March 18, 2022

And got lots of useful resposnes. Rather than compile them here if interested people should browse the responses.

The ongoing disaster of the new UC Health Insurance Pharmacy "benefits"

Recently I posted to Twitter about the disastrous new University of California Pharmacy Benefits system.

Dear @UofCalifornia @ucdavis

This is NOT OK.

I just got a notice by letter in mail that my insurance will no longer cover the insulin I have been getting "as of January 1, 2022". Letter was dated in February and was received after March 1, 2022.

This is NOT OK.

— Jonathan Eisen (@phylogenomics) March 7, 2022

In summary, I got a letter in March that warned me of something that was about to happen in January (that is, in the past).  And what was about to happen was bad - cutting off coverage of my insulin.  And the system in place for trying to even find out what was going on and what to do about this was a disaster.

I note, this generated an enormous response and it was clear that this was not just me experiencing the disaster of their system.

I used the threadfreader app to make this into a more easily readable thread here: https://threadreaderapp.com/thread/1500934973775249412.html

A few people pointed me to some contacts at UC Davis to reach out to and I did.  They were both great and very helpful.  They told me that the UC was working on dealing with many of these issues and some of those responses were rolled out quickly. 

And I posted about how these efforts were sort of helpful but not ideal. For example

Well, the saga continues -- just got this from Navitus. They say I "may be eligible" for an extension of 1 bonus month with my prior prescription. Pretty useless to be honest. pic.twitter.com/ASUHvYuUwn

— Jonathan Eisen (@phylogenomics) March 14, 2022

On March 21, I got a detailed email from the University of California apologizing for the situation and detailing many changes to apparently try and help fix things.  I mean, they never should have done this and used this incredibly cheap, low grade system.  But at least they are trying to fix things.

Below is the email from UC. More about this in a bit but I wanted to share the full text for people to see here.

An important message from UC about your pharmacy benefits

Dear Jonathan,

We are writing to acknowledge — and apologize for — the problems many members of the UC community are experiencing with Navitus Health, a new administrator of pharmacy benefits for UC employee and Medicare PPO plans, and to let you know what we are doing to fix the problems.

Last year, University of California Health (UCH) and UC Systemwide Human Resources selected Navitus Health to administer pharmacy benefits, starting Jan. 1, 2022. This decision was made following an extensive formal bid process, conducted by a committee with representatives from UCH, Systemwide HR, UC faculty with pharmacy expertise and UC’s retiree association. 

Navitus was selected as the partner that could provide UC with the best overall flexibility, service, and affordability. However, since UC’s transition to Navitus Health, we have heard from too many members who have been negatively impacted by this change. 

Some members have had to change prescription drugs, been required to complete time-consuming authorization processes and experienced denials by Navitus, causing unnecessary anxiety and frustration. Navitus failed to meet the scheduled target date for mailing a clinical transition letter, causing hardship and worry for faculty, staff, retirees and their family members.  

Additionally, like many employers Navitus has faced customer service staffing challenges, leading to wait times that far exceed Navitus’ standards and UC performance guarantees. Among other things, this has put undue pressure on benefits professionals at UC locations and in the UC Retirement Service Center and the UCPath Center, as they have worked to provide support that should be handled by Navitus.

We take these problems — and our responsibility to ensure that members of UC health plans have access to the prescriptions they need — very seriously. UCH and UC Systemwide Human Resources have been in constant communication with Navitus, and we want to let you know what we are doing to fix these problems.

Support with member transitions

• Due to the delay in mailing clinical transition letters, Navitus has provided an extended transition period to the end of April for drugs that are not covered. Extension letters and an email campaign were recently initiated.
• Navitus will call members who need to transition to new medications directly and offer help with authorizations, denials, and appeals. Those who have experienced a denial for a Not Covered/Non-Formulary medication will also receive a phone call offering help. 
• UCH, Alliant (a UC consultant) and Navitus will audit and review the protocols Navitus uses for denials to ensure they are in alignment with Navitus internal guidelines, industry standards and Medicare guidelines – and to identify and correct any gaps. 

Customer service improvements

• Navitus has committed to adding an additional 35 customer service representatives (an increase from 125 to 160) by the end of April, and hopes to add another 15 staff after that, along with additional support for UC benefits professionals.
• Navitus has also added two more personnel with pharmacy clinical expertise to help UC benefit professionals support members.
• In addition, Navitus is exploring a concierge-type customer service model to ensure UC members receive the dedicated assistance they need.

Again, we sincerely apologize for any difficulties you or your family members have experienced during this transition. We are committed to you receiving the critical health care you deserve, without unnecessary inconvenience or frustration.

Sincerely,

 

Cheryl Lloyd                                                    Dr. Carrie Byington

Vice President                                                 Executive Vice President

Systemwide Human Resources                      University of California Health

Please do not reply to this message. Replies to this message are routed to an unmonitored mailbox. 

Baby Hummingbirds at Yolo Bypass

 

So I got a glimpse of a hummingbird nest at Yolo Bypass

Hummingbird sitting in nest at #yolobypass - thanks to @ucdavis Prof. David Rizzo and wife who I bumped into and who pointed it out pic.twitter.com/qHRxfz2Fgl

— Jonathan Eisen (@phylogenomics) March 6, 2022

And this was amazing for me - might be 1st hummingbird I have seen in field on a nest since 1988 when I studied Broad tailed hummingbirds at @RockyMtnBioLab with Bill Calder

— Jonathan Eisen (@phylogenomics) March 6, 2022

Here are a few higher resolution pics (now that I got home) pic.twitter.com/2HXkxJmSKc

— Jonathan Eisen (@phylogenomics) March 6, 2022

And then I went back and got a better look at it , with babies ...

Follow up from a few days ago ..

Baby
Hummingbirds
In
Nest

I did not want to disturb so stayed really far away (this is cropped and was taken with a 500 mm lens)

But still -- OMG OMG OMG https://t.co/DboPEDSfkP pic.twitter.com/ceI3HnQa1Z

— Jonathan Eisen (@phylogenomics) March 18, 2022

And I posted some videos too

A field guide to SarsCOV2

 

Gave a talk on SarsCOV2 to the Yolo County Community of Practice group. I basically discussed how the concept of a field guide can be useful for thinking about SarsCOV2. Here are my slides

A Field Guide to Sars-CoV-2 from Jonathan Eisen

I will try to post the recording of the talk at some point.

Northern Harrier at Yolo Bypass

 Some pics ...

Best Pics from Nimbus Fish Hatchery

Went to Sacramento for a Doctor's appointment and then had a 2 hour Zoom call. Decided to do the call while walking around the Nimbus Fish Hatchery which I have never been to. I heard that people had seen a rare duck there so went on over. And it was awesome. I then messaged a grad student in my lab, Alonna Wright who lives nearby and she came over for a walk after lunch. Here is a link to a slideshow of some of the pics I got

Some thoughts on Omicron and COVID19 in the last week or so

 

Some recent Tweets and threads from me on Omicron and related topics

I am dismayed by the people, including leaders, who are treating #Omicron as "mild" & therefore not a big deal ignoring the unvaccinated & unboosted, long covid, at risk groups and that it is not "mild" for everyone, just on average has less severe effects to the vaccinated

— Jonathan Eisen (@phylogenomics) January 5, 2022

If you are citing something written by Monica Gandhi on COVID please read this and other threads pointing out just how many times she has been wrong wrong wrong and wrong. https://t.co/XJcJ2kytlt

— Jonathan Eisen (@phylogenomics) January 6, 2022

Looking for guidance on how to wear / test / optimize the fit of KN95s and N95 masks.

— Jonathan Eisen (@phylogenomics) January 6, 2022

Honestly, disappointed in @Bob_Wachter calling this "new". We knew this >1 month ago. https://t.co/8UqtflU7WF

— Jonathan Eisen (@phylogenomics) January 6, 2022

Repeat after me.

It is not the flu.
It is not the common cold.
It is not mild.
It is not something to just let rip.

It is something we can and should keep fighting. https://t.co/any0vRZWwr

— Jonathan Eisen (@phylogenomics) December 31, 2021

And the @ucdavis #COVID #s and positivity rates are going up up up up up up up. https://t.co/VsqgJYyw0C

And remember, many people are away right now so, well, the #s when people return will likely be very much higher pic.twitter.com/x6cE3sKnbB

— Jonathan Eisen (@phylogenomics) January 1, 2022

Tribute to EO Wilson

 

When I was a senior at @harvard in 1990 I started an "Environmental Issues" journal as part of activities leading to the 20th anniversary of Earth Day. I hoped to get EO Wilson to be our faculty sponsor. I phoned his office and arranged a meeting with him via his assistant 1/n https://t.co/0fyvH0ykky

— Jonathan Eisen (@phylogenomics) December 27, 2021

Video and slides of my talk for the Microbiome Virtual International Forum posted

I gave a talk last week for the Microbiome Virtual International Forum. https://www.microbiome-vif.org/ Title: Evolution of microbiomes and the evolution of the study and politics of microbiomes (or, how can something be both ridiculously overhyped and horrifically underappreciated)" 

 See the Youtube video:  

 Slides:

Evolution of microbiomes and the evolution of the study and politics of microbiomes (or, how can something be both ridiculously overhyped and horrifically under-appreciated) from Jonathan Eisen

Also see this Twitter thread for some more info:

OK so I gave a talk for the @MicrobiomeVIF tonight https://t.co/4fJ4n6AJE6. I think it went, well OK, but it was really hard for a few reasons ... 1/n

— Jonathan Eisen (@phylogenomics) December 8, 2021

Slideshow of Otters at the UC Davis Riparian Preserve

Made a slideshow of the otters I saw at the UC Davis Riparian Preserve yesterday. See

Videos of Talks from the JGI "NeLLi (New Lineages of Life)" Meeting Now Available

Recently the DOE JGI Hosted the "NeLLi" meeting on New Lineages of life.  See agenda here: https://usermeeting.jgi.doe.gov/2021-nelli/2021-nelli-agenda/ 

There were a whole series of interesting talks in this program and now the videos are available on Youtube. 

See Youtube Channel or the embedded video link below.

Wall Street Journal Podcast on the Downfall of uBiome, part 1 and 2

Part 1 of "The Journal" podcast featuring story by Amy Marcus et al on the downfall of uBiome.  Includes interviews with multiple people including myself.

What went wrong at uBiome, Part 1. 

 

Part 2 has now been posted

 

Some recent posts of interests from my lab blog and MicroBEnet

So I have been lax in blogging these days as I spend a lot of time on Twitter. And when I do write blog posts, I don't always post here - I also post blog posts to a few other places including my lab blog and the microBEnet blog. Here are a few moderately recent posts from these places

Lab Blog

• The tale of the blue soy products – from contaminated soy milk to a new publication
• The Benefits (and Occasional Drawbacks) of Integrating Evolutionary and Genomic Studies (talk video and slides)
• New paper from the Eisen lab (with many others) on Global biogeography of chemosynthetic symbionts

microBEnet blog

• Metagenomic Binning / Assembly
• Wanted: Workers for the COVID19 Mass Testing Operations for UC Davis and Healthy Davis Together 
• Compiling Information about COVID19 transmission, masks, filtration, schools, etc.
• Wanted – science driven guidelines for deciding if and how to keep open / reopen schools re: #COVID19

Some thoughts on the CDC new mask guidance

 

See this thread 

I am with @kprather88 here. Really vexed by what @CDCDirector and @CDCgov have done here. I mean, I get the general idea of trying to return to normal and encourage vaccination. But here are some thoughts for why I am still a bit vexed. https://t.co/tTzdFYoTqU

— Jonathan Eisen (@phylogenomics) May 14, 2021

Made into a thread reader thread here: https://threadreaderapp.com/thread/1393025234303741954.html 

Compiling some of my Twitter comments about the evolution and origins of SarsCoV2/ COVID19

 News Stories Quoted in

• UC Davis Aggie: Emerging SARS-CoV-2 variants raise concern for the future of the pandemic
• 9/15/2020. Newsweek. Fact-check: Does a New Study Give Evidence that the Coronavirus Was Made In a Lab?
• May 17, 2020. Newsweek: Scientists Shouldn't Rule Out Lab As Source of Coronavirus, New Study Says
• April 27, 2020. The controversial experiments and wuhan lab suspected of starting the coronavirus pandemic. Newsweek. 

Twitter Threads

---

Relating to the lab vs natural origin theory of #SarsCOV2. I would like to call attention to the history of the anthrax attack investigation. Circumstantial evidence, that seemed so strong to so many people, was used to falsely accuse multiple people. https://t.co/olpDu8sKT9

— Jonathan Eisen (@phylogenomics) March 27, 2021

---

Reading: Why the COVID lab-leak theory in Wuhan shouldn't be dismissed

By ⁦@alisonannyoung⁩ in ⁦⁦@USATODAY⁩ . #covid19 https://t.co/u42TxLOcHe

— Jonathan Eisen (@phylogenomics) March 22, 2021

---

This is a fascinating deep look into theories about the origins of #B117 #SARSCoV2 variant:

A lone infection may have changed the course of the pandemic https://t.co/jKNgWth63T

By @mattsreynolds1 w/ comments from @EvolveDotZoo, @LauringLab @firefoxx66 @GuptaR_lab @jcbarret

— Jonathan Eisen (@phylogenomics) February 10, 2021

---

Worth reading / rereading - on the risks of gain of function research from 2014 from The Cambridge Working Group #covid19 #GainOfFunction https://t.co/PfTd32nNHe

— Jonathan Eisen (@phylogenomics) May 19, 2020

---

Yes, as I told @newsweek it is theoretically possible that a Chinese lab accidentally released #SARSCoV2 https://t.co/90qFnFcKJc but preponderance of evidence so far supports all natural events and the evidence actually supporting "lab release" is shown in this pic #Covid19 pic.twitter.com/TyqAiFnQuf

— Jonathan Eisen (@phylogenomics) May 3, 2020

---

Reading: Scientists shouldn't rule out lab as source of coronavirus, new study says https://t.co/cZIyRXczrY - personally I do not find the analysis in this new paper remotely convincing 1/n

— Jonathan Eisen (@phylogenomics) May 17, 2020

New article out from the Eisen Lab: Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum

See Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum 

Paper based on PhD thesis work of Katie Dahlhausen and wrap up of analysis led by Laetitia Wilkins. 

Full citation:

Dahlhausen KE, Jospin G, Coil DA, Eisen JA, Wilkins LGE. 2020. Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum. PeerJ8:e10177 https://doi.org/10.7717/peerj.10177

Acknowledgements. We thank Céline Caseys ORCID: 0000-0003-4187-9018 for her idea to search eggNOG annotations against KEGG Class 1.11 Xenobiotics biodegradation and metabolism pathways; Chris Brown ORCID: 0000-0002-7758-6447 for his script to download assemblies in batch from GenBank; Cassandra L. Ettinger ORCID: 0000-0001-7334-403X for valuable comments on the pangenome analysis and help with revising the figures. We also thank Dr. Joseph Gillespie ORCID: 0000-0002-5447-7264, Dr. Raphael Eisenhofer ORCID: 0000-0002-3843-0749 and two anonymous reviewers for comments on the submitted manuscript. Isolate 16S Sanger sequencing was performed at the UC Davis College of Biological Sciences DNA Sequencing Facility.

Green heron at Yolo Bypass

View this post on Instagram

Green heron at #YoloBypass today #nature #birdphotography

A post shared by Jonathan Eisen (@phylogenomics) on Sep 20, 2020 at 7:11pm PDT

Great horned owl at #YoloBypass

 

Went for a walk at Yolo Bypass 8/23/2020 early in the AM and got a nice view of a Great Horned Owl. Here are some pics.

Introducing "Hammerhead Man" - the superhero you did not know you needed.

So I was digging through some old school papers because my daughter asked me what books they had use write reports on in high school and, well, I have a lot of my English papers from high school in a box in a closet.  

And in digging through this box I found a short story I wrote for a creative writing class from freshman year in college, which was taught by Catherine Tudish. 

Now, mind you, I was not in a good place when I wrote this as I was reading from the death by suicide of my father.  And, possibly related to that I truly have almost no memory of writing this, other than the concept of the assignment. But I read it to my kids. And, well, I actually like it.  It has a lot of issues.  But I think it should be expanded on. I may just revisit this.

So - here is the official first release of "Hammerhead Man".  With corrections and comments from Catherine Tudish. 

Brief summary of the gear I use for photography (of mostly birds)

So - many people have asked what gear I use for my photography (mostly of birds). Here is a quick summary. See some of my pictures here: https://jonathaneisen.smugmug.com



Camera: Nikon D500




 Lenses Birding: Nikkor 200-500 f/5.6
 

 Macro: Nikkor 105 mm f/2.8
 


Based on review of Mark Smith.

See more detail in this blog post here. "Stalking the wild garganey in West Sacramento #birding #eBird #iNaturalist #birdphotography #nikonD500.

Slides I have used for "Biodiversity and the Tree of Life" at @ucdavis

I have posted the slides I have used so far in remote teaching for "Biodiversity and the Tree of Life" - aka Bis2C - at UC Davis and I thought I would share them here.

Many of the figures are from "Life v 11" by Hillis et al. which is the textbook we have been using for the class. I have been told in the past by the publishers that this was OK to do so I am assuming it is still OK. Hope there are not too many errors ... for some reason Lecture 10 will not upload - working on it

BIS2C_2020. Lecture 6. The Tree of Life. from Jonathan Eisen

BIS2C_2020. Lecture 7. The Domains of Life. from Jonathan Eisen

BIS2C_2020. Lecture 8. Phylogenetic Diversity of Microbes from Jonathan Eisen

BIS2C_2020. Lecture 9. Form and function from Jonathan Eisen

BIS2C2020 - Lecture 10 - Parasites and Pathogens from Jonathan Eisen

BIS2C_2020. Lecture 11 Viruses and gene transfer from Jonathan Eisen

Lecture 12 - Mutualisms and Microbiomes - BIS2C from Jonathan Eisen

BIS2C_2020. Lecture 13 Organelles and Endosymbiosis from Jonathan Eisen

BIS2C_2020. Lecture 22 Fungi Part 1 from Jonathan Eisen

BIS2C_2020. Lecture 23 Fungi Part 2 from Jonathan Eisen

Today's stay at home activity - virtual tour of the Dali museum

Love that the Dean of the College of Biological Sciences Mark Winey sent out a suggestion to check out this virtual tour of the Dali Museum in his regular message to the college.  And it is pretty cool. Check it out: Visit the museum as you have never done before! | Fundaci� Gala - Salvador Dal�

Another #NatureAtHome project: Never Home Alone:

This is another nice at home activity relating to Nature.  Rob Dunn and colleagues have been running this  Wildlife of Your Homes project in various ways for many years.  And it is easy to participate in it via iNaturalist. Take pics of bugs or other critters in your home and then post them and add them to the iNaturalist project.  See Never Home Alone: The Wild Life of Homes � iNaturalist.

Another #NatureAtHome project: Never Home Alone:

This is another nice at home activity relating to Nature.  Rob Dunn and colleagues have been running this  Wildlife of Your Homes project in various ways for many years.  And it is easy to participate in it via iNaturalist. Take pics of bugs or other critters in your home and then post them and add them to the iNaturalist project.  See Never Home Alone: The Wild Life of Homes � iNaturalist.

Resource for #NatureAtHome: California Academy of Sciences

OK have not been posting much to this blog for a few weeks due to the disruption from the coronavirus but I am going to start posting again when I find things that may be of use for the new world of social distancing, etc.



Today I am posting about the California Academy of Sciences which has a nice page compilation information and resources they have for activities at home: Academy @ Home | California Academy of Sciences



Thanks Cal Academy.

Collecting some of my comments about Sacramento County's poor response to COVID19

Posted this rant on March 9

This does not seem like a good plan: "Sacramento County Announces New Mitigation Efforts COVID-19" https://t.co/5W3Dv4Lqr9 #COVID19 #Coronavirus - especially the plan to shift from containment to mitigation #Sacramento cc: @sacbee_news 1/n pic.twitter.com/dYUwEoUGb1

— Jonathan Eisen (@phylogenomics) March 9, 2020

And then another rant

I think the Sacramento plan is problematic - if they are correct that it is time to ditch containment and move to mitigation then why is their mitigation plan among the weakest announced anywhere ? See https://t.co/mHnvLbdGGG https://t.co/mHnvLbdGGG

— Jonathan Eisen (@phylogenomics) March 10, 2020

And this one

But couldn't you do quarantine for some people but not necessarily for health care workers?

— Jonathan Eisen (@phylogenomics) March 10, 2020

And then Placer and Yolo County came out with their somewhat more aggressive plan

So #Yolo and #Placer counties have announced that they are also stopping containment efforts. I still think this is a bad idea but at least compared to #Sacramento county these counties are at least pushing the mitigation strategy a bit more strongly. See https://t.co/pbtsOMbmGN https://t.co/ZZlO2NtmFX

— Jonathan Eisen (@phylogenomics) March 10, 2020

And more

The Sacramento County plan is a joke - 1) containment is still useful in some cases, they should not ditch it 2) their plan for mitigation (reducing community spread) is the most limited of any place I have seen in the country -see https://t.co/ZZlO2NtmFX

— Jonathan Eisen (@phylogenomics) March 11, 2020

And this

Brutally behind the curve - Sacramento’s public health leader - Q&A: Sacramento’s top health official on what’s being done to stop the coronavirus outbreak https://t.co/enebtjqNkK

— Jonathan Eisen (@phylogenomics) March 15, 2020

And another

So - I went through the #Sacramento County plan for dealing with #COVID19. It is bad. https://t.co/ek99YNBzSw

— Jonathan Eisen (@phylogenomics) March 10, 2020

And this

Really incredibly important and calls into doubt the inane claims from #Sacramento, #Yolo and other local counties that we have to stop contact tracing and other containment actions https://t.co/qp5rE3uACg

— Jonathan Eisen (@phylogenomics) March 11, 2020

And another

Really disappointed in #Sacramento health director’s approach: Sacramento County Health Director Defends Coronavirus Strategy, Says Lack Of Tests Made Containment Impossible - https://t.co/tiWN9gGBkS https://t.co/nqikmcSc67

— Jonathan Eisen (@phylogenomics) March 14, 2020

And another

Really great article by @edyong209 about some of the problems with the UK #covid19 strategy and communications; sadly some similar things have been going on here in #Sacramento area https://t.co/jtdVqkfPel

— Jonathan Eisen (@phylogenomics) March 16, 2020

My posts about #UCDavis and #Covid19

Going to use this page to keep track of some of what I have been posting about what is going on at UC Davis in regard to the coronavirus.  Will add more later ... but just going to use this to keep track.

February 26

Things blew up at @ucdavis with reports that the 1st community acquired case of COVID19 was at our hospital. I received an email about this that I eventually posted to Twitter (I waited to post until I saw others reporting this)

Email I received earlier today from @ucdavis Medical Center leaders regarding the case of apparently community acquired #COVID19 in #Sacramento at #UCDavis hospital pic.twitter.com/q9qrJq5iWo

— Jonathan Eisen (@phylogenomics) February 27, 2020

Tons of stories came out over the next few weeks about this and I will add some links to them. But eventually, attention went elsewhere as the 1st large clusters of cases that were detected in the US ended up being in other locations.

March 7.

Actions from UC Davis announced regarding COVID19 was, well, better than nothing but pretty limited.

Announcement from @ucdavis re: #ucdavis #COVID19 #Coronavirus #SocialDistancing:

Will help increase social distancing but not going as far as I would like ... I hope this moves very soon from "recommend" to "require" https://t.co/khnnVCZFeN

— Jonathan Eisen (@phylogenomics) March 8, 2020

Important announcement from @ucdavis: not as far as I would like but will help increase social distancing; hope they move from "encourage" to "require" soon ... #ucdavis #COVID19 #Coronavirus #SocialDistancing https://t.co/sqjGXO3fqF

— Jonathan Eisen (@phylogenomics) March 8, 2020

March 10. 

UC Davis expanded actions.

Major new actions from @ucdavis regarding #COVID19 #Coronavirus h/t @TLowePower https://t.co/NLOLw2EaH0

— Jonathan Eisen (@phylogenomics) March 10, 2020