Friday, May 05, 2023

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.

Monday, April 03, 2023

Responses to question about functional annotation of metagenomic reads

Posted a question to a few places

Thursday, January 19, 2023

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

Monday, December 19, 2022

Well, this is about as scammy / spammy as a journal can get ... putting me on an editorial board I did not agree to be on ...

 So I got an email this AM from "Microorganisms Editorial Office"

Dear Prof. Dr. Eisen,

We are pleased to inform you that your information has been announced on the 
webpage of our journal's board.

Please check that all of your information is correct here:

Cool. Cool. Except I never agreed to be on their editorial board. And yet there I am on their web site.

Prof. Dr. Jonathan Eisen Website  Editorial Board Member  Professor, Department of Evolution and Ecology, University of California, Davis (UC Davis), Davis, CA, USA Interests: comparative genomics; next generation sequencing; molecular evolution; bioinformatics and computational biology; genome sequencing; genome annotation; metagenomics; genomics; molecular phylogenetics; science communication

No MDPI Microoorganisms. This is not OK. 

Sunday, September 11, 2022

Lake Arrowhead Microbial Genomics Meeting History

Making a page here with information on the history of the Lake Arrowhead Microbial Genomes meeting.  Please post in comments any additional links to other information.

Friday, August 19, 2022

Wanted - comments on the current @ucdavis COVID plans

 So - I have been publicly and privately critical of some of the recent @ucdavis practices regarding COVID. If you want to know more about my areas of concern see for example this Twitter thread which I posted today: 

After I posted that, The Chancellor of UC Davis Gary May posted an article with some details of current UC Davis COVID plans. See 

What he wrote is below - but rather than comment myself right now, I am wondering - what do people out there (especially those at UC Davis) think of all of this?


Davis campus students are required to be compliant with the UC Vaccine Policy by Sept. 21 either by being up to date on vaccines and boosters or submitting a religious or medical exception request. Students who are not in compliance by Sept. 21 will receive a registration hold on their accounts for fall quarter. Please visit the Information for Students and Families page on the Campus Ready website for additional details about the vaccine policy compliance process. The vaccine policy also applies to employees.

It’s clear that COVID-19 will be with us for some time. UC Davis continues to monitor for the virus through weekly wastewater testing, which helps inform our decision making. We have reviewed the scientific literature and heard from many people, and, at this point, we are not likely to increase the frequency of wastewater testing given that Davis is not a large urban center. Also please note: We have access to daily test results from Stanford’s Sewer Coronavirus Alert Network (SCAN).

We encourage our students, faculty and staff to get tested regularly for COVID-19. The Davis campus testing kiosk — offering free, asymptomatic testing (saliva-based) — remains in operation, although in a new location: Human Resources Administration Building (1050 Blue Ridge Road), across La Rue Road from the ARC. The kiosk is open from 8:30 a.m. to 4:30 p.m. Sunday through Thursday (closed Fridays and Saturdays). Testing is by appointment only through the Health-e-Messaging portal. Please note: Testing appointments are limited from Sept. 13 to 15, due to move-in.

At-home antigen tests are available for free as follows:

  • By mail from the federal government.
  • From no-charge vending machines around Yolo County. The machines are accessible 24 hours a day at the Mary L. Stephens Davis Branch Library, 315 E. 14th St.; West Sacramento City Hall, 1110 W. Capitol Blvd.; Winters City Hall, 318 1st St.; and Esparto Regional Library, 17065 Yolo Ave. (with one more to be installed in Woodland).
  • From Yolo County libraries during open hours.

I would also like to recognize the effects of long COVID and the impact it continues to have on people. We are learning more about it every day, in UC Davis Health’s Post-COVID-19 Clinic, which opened in November 2020; and in our research and clinical studies, including one assessing the risks for children.

Students affected by long COVID should work with the Student Disability Center for resources and support. Employees should work with Disability Management ServicesThese units are busy, so please reach out to begin the interactive process as soon as you can.

Masking and air filters

I recognize that there is still some anxiety about masking. While the Davis campus does not have a mask mandate in place, we strongly recommend that people wear masks indoors to reduce risk.

Free masks are coming soon. The university plans to distribute one N95 mask to every student and employee this fall quarter, with this one-time distribution to take place in September. For more information about the distribution, students should contact their major departments, and employees should contact their departments or units. See “Directions for departments” on how to acquire mask supplies.

Remember that a proper mask fit is especially important. A 10-minute video is available for students on how to properly use N95 masks, also called respirators. They are rated to filter out 95% of particles.

Employees are required to complete a 10-minute video training about the proper use of N95 masks.

Yolo County also offers video guidance on masking. Further information can be found at Campus Ready and through the California Department of Public Health.

If you’re concerned about air filtration at home, a Corsi-Rosenthal Box is a cost-effective device that can be built with just a few components. The box was co-invented by Richard Corsi, dean of the College of Engineering, and has received acclaim nationwide. Visit this link to learn how to build your own Corsi-Rosenthal Box.

Sunday, June 05, 2022

Most recent post

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 "...