Category: Misc.

MUTATOR: The perfect “vanity” plates for me, to pay homage to some key people

Well, so I got a new car a little while ago. And though I had had personalized plates for my previous vehicle (“PLOS ORG”), I was not planning to get ones for this vehicle. And then I had a conversation in the hall about personalized plates that a colleague of mine has, and I was intrigued.

So I went to the California site where you can search for whether or not specific personalized plates are available, and I searched for a variety of possibilities. Some were available. Some were not. And then I decided to try one that I just figured would not be available. But amazingly, it was.

This personalized plate, which some call “vanity” plates, is a perfect way for me to acknowledge some people who have played very very important roles in my life and career.

The plate reads “MUTATOR”. And this is really quite good for me to pay tribute to many people including

California license plate reading "MUTATOR"

1. My wife, Dr. Maria-Ines Benito who worked on the Mutator transposable element in corn for her PhD. (e.g. see Characterization of the maize Mutator transposable element MURA transposase as a DNA-binding protein). I note – I even ended up co-authoring a paper with her and Ginny Walbot (see below) on Mutator, defining the Mutator family of transposable elements, so the MUTATOR plate works for me too. See Sequence similarity of putative transposases links the maize Mutator autonomous element and a group of bacterial insertion sequences.

2. My wife’s PhD advisor Ginny Walbot, who is one of the grand gurus of studies of the Mutator transposable element (see more here).

3. My PhD Advisor Phil Hanawalt who introduced me to DNA repair and mutation processes and mutator genes supported me as I worked extensively on evolution of “mutator” genes including MutS and MutL. See for example A phylogenomic study of the MutS family of proteins and A phylogenomic study of DNA repair genes, proteins, and processes.

4. Jeffrey H. Miller who did pioneering work on mutator genes in E. coli and other organisms (see some detail here) and who also helped build my career in various ways including by organizing and then eventually inviting me to co-organize the Lake Arrowhead Microbial Genomes meeting.

5. Richard Lenski who has done spectacular work on microbial evolution and on the role that mutator strains / mutations play in such evolution. In addition to being a great colleague over the years, he helped transform my PhD work via an interaction at a Gordon Conference when I was working on adaptive mutation in E. coli.

So, yes, the “MUTATOR” license plate is a bit about vanity for me. I think it is cool. I like to think of myself as a “MUTATOR” in various ways and I also have done work on and off again on mutation processes and mutator strains and genes. But really, the best part for me is that it pays tribute to my wife and a collection of great scientists who helped shape my career.

Elephant Seals at Point Reyes

So I went to Pt. Reyes this past weekend. And among many things I got to see elephant seals for the first time in my life. They were mesmerizing. I took a lot of pics. Here are some, all from the Drake’s Beach area.

For some of the “Scenes” I made gifs from a series of pics to show some motion …

The Big Male

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Chimney Rock Area

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And one bonus seal …

Compiling Some 2019 posts of mine about Jeffrey Epstein, Scientists, and Harvard

Compiling some posts of mine from a few years back where I dug into some of the ties between Jeffrey Epstein, Harvard, and some scientists. There have been lots of really good articles and posts about the sordid connections involving Epstein. I am compiling this simply because I spent a lot of time digging into the Internet Archive and Papers and Website of Epstein and others at the time and want to make a record of this information.

August 22, 2019

See Thread here: https://twitter-thread.com/t/1164549482798653440

@phylogenomics-When, if ever, will @DrMANowak and @harvard do something about their unethical association with rapist Jeffrey Epstein – they took his money, propped up his reputation, and now? crickets – read more from @xeni about this_ https__…-2Download

August 25, 2019

Thread Here https://twitter-thread.com/pdf/1165639530235355138

@phylogenomics-Over the last few days, I have spent some time digging into the sordid connections between rapist _ pedophile Jeffrey Epstein and various groups at @harvard e.g., https___t.co_UAwjqbhh6t by @phylogenomics(Jonathan Eisen)-twitter-thr…Download

Sept. 12 2019

See thread here https://twitter-thread.com/t/1172326369897828355

@phylogenomics-Letter from @harvard President to affiliates (e.g., alumni like me) regarding funding from Jeffrey Epstein #NotImpressed https___t.co_MhCRo6Q25z by @phylogenomics(Jonathan Eisen)-twitter-thread.comDownload

Sept. 22, 2019

Thread: https://twitter-thread.com/t/1175795079434235904

@phylogenomics-Call me unimpressed w_ @harvard here_ %22Harvard Office of the General Counsel to Review Epstein Donations%22 https___t.co_dMKFyn5Z8E 1_n by @phylogenomics(Jonathan Eisen)-twitter-thread.comDownload

September 25, 2019

Thread: https://twitter-thread.com/t/1176859576265654272

@phylogenomics-Call me unimpressed w_ @harvard here_ %22Harvard Office of the General Counsel to Review Epstein Donations%22 https___t.co_dMKFyn5Z8E 1_n by @phylogenomics(Jonathan Eisen)-twitter-thread.comDownload

November 16, 2019

Thread here: https://twitter-thread.com/t/1195731985685024768

@phylogenomics-Two months ago the president of @harvard put out a self-serving statement about ties to #JeffreyEpstein promising all sorts of %22reviews%22 of those connections – and since then – nothing – what a joke – clearly plan is to try to wash …Download

December 14, 2019

Thread Link https://twitter-thread.com/t/1205875157736157185

@phylogenomics-Reading_ Jeffrey Epstein spent over $500,000 to fund never-completed episodes of a PBS science series the year before sex trafficking charges https___t.co_D7qSTdNIN7 and look – a nice $50,000 to the Edge Foundation https___t.co_YSN8…Download

September 2, 2020

Am I too gullible?

So I posted a week or so ago about how I wanted to learn how to ID white headed gulls this year. And I asked for suggestions / advice on how to learn and got some useful tips so I am sharing them here.

Here are some of the posts and responses I got:

Posted to BlueSky

OK I know this will be one of the craziest things I have ever posted, but in 2025 I have decided I really want to learn how to identify seagulls. Suggestions for best places to start learning would be welcome. #birds

— Jonathan Eisen (@phylogenomics.bsky.social) 2025-01-19T17:57:16.596Z

http://www.allaboutbirds.org/guide/browse…

— Tom Buckner (@justanotherant.bsky.social) 2025-01-19T22:58:48.024Z

I think out on the west coast of the US that’s a particularly tricky challenge! There’s an excellent new photographic guide for N. American gulls – press.princeton.edu/books/paperb…. Also @alvarosadventures.bsky.social is based out there and runs excellent gull ID workshops!

— Liam Langley (@liamlangley1.bsky.social) 2025-01-20T09:18:59.489Z

nice! for one, the best NA field guide ever was recently published here: http://www.amazon.com/Gull-Guide-N…As for process, pick the 1-3 most common species in your area and study them exhaustively, when something odd shows up, it will stick out.

— Andy Boyce (@andyjboyce.bsky.social) 2025-01-19T18:07:20.650Z

And Also Posted to X

And on Facebook got some really good suggestions

A friend from high school pointed me to Jack Laws and all his amaxzing materials including https://johnmuirlaws.com/gull-identification-guide-free-download/

Another person pointed me to this book: https://www.amazon.com/Gulls-Simplified-Comparative-Approach-Identification/dp/0691156948

And someone else pointed me to this: https://thecottonwoodpost.net/2023/10/12/gull-identification-in-puget-sound/

New paper out from studies of metagenomes from Tramway Ridge in Antarctica

I am a co-author on a new paper that just came out.

Nutritional niches of potentially endemic, facultatively anaerobic heterotrophs from an isolated Antarctic terrestrial hydrothermal refugium elucidated through metagenomics. Craig W. Herbold, Stephen E. Noell, Charles K. Lee, Chelsea J. Vickers, Matthew B. Stott, Jonathan A. Eisen, Ian R. McDonald & S. Craig Cary. Environmental Microbiome volume 19, Article number: 104 (2024)

Figure 1 from the paper.

This came from a long ago collaboration in which I was involved with the lab of Craig Cary, who very sadly passed away recently. I got to know Craig from working with him (and Barbara Campbell and others) on a genome project in the late 2000s (see Adaptations to Submarine Hydrothermal Environments Exemplified by the Genome of Nautilia profundicola. PLoS Genet 5(2): e1000362). While we were working on that project, Craig and Ian McDonald contacted me about a proposal they were putting together to do some sequence based studies of microbes from Mt. Erebus in Antarctica. I became a collaborator on their project and their grant was funded in late 2008. Anyway – long long story. Eventually, Craig and others planned a trip to Erebus and alas I was unable to go but a post doc in my lab Morgan Langille was able to join them. And around that time Craig (Cary) hired Craig (Herbold) to work on the project. And the Craigs did multiple things but the part of the project in which I was to be involved did not happen immediately.

But then Craig Herbold moved to New Zealand in the beginning of 2024 and he and Craig Cary resurrected the project. And Craig H. and others (with a little bit of input from me here and there) wrote up the paper that I describe above.

Very sadly, in March Craig Cary passed away. For me, this paper is in his honor. Craig Cary was one of the people who really got me interested in broad studies of microbial diversity from all environments.

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.  

Eisen.Talk.Sequencing-and-MicrobesDownload

My talk for #LAMG2024 – Lake Arrowhead Microbial Genomics 2024 meeting

So I have a talk last night as part of thr introduction to the Lake Arrowhead Microbial Genomics 2024 meeting (aka #LAMG2024). It was kind of a comedic rendition of the history of the meeting with some comments on this years meeting.

Here is a PDF file of my slides

Eisen.LAMG2024Download

Will post some more about the meeting later, but am actually listening to a talk right now so got to go back to that.

Cooper’s hawk calling at UC Davis – found with a little help from Merlin

Was at the end of a bike ride to work yesterday and was biking by the UC Davis Vet School when I heard a screeching bird. I was not sure what it was but I knew I had heard something like it before and also that it was not common.

So (1) got off my bike (2) got out my iPhone (3) opened the Merlin App and (4) starting the “Start New Recording” option and very quickly it IDd the bird as a Cooper’s hawk.

So then I got out my camera (I had brought a relatively new travel camera – a Nikon CoolPix) with me on my ride and had been taking pics along the way but put it in my backpack when I got near the Vet School – assuming incoorectly I would not want to take any more pics now that I was close to my office).

And I tried to figure out where the call was coming from. It took a bit but I found the bird and first made a video with my phoen and then took some pics. They are below.

A Semi-Random Day of Mammals

So I got up really early on July 12th to get out and go to Yolo Bypass to go for a hike before it got too hot. The weather prediction was for it to get to above 110 °F so I really wanted to get out early. And I was really looking forward to see what creatures were out early in the AM

I left my house jsut before 6 and the sun had already risen but was quite orange still.

Possibly A Blue Grosbeak Seen on the Way to Yolo Bypass

And then when I got there, alas, the gate was closed, even though it is supposed to be opened at sunrise.

Gate at Yolo Bypass Closed

There was also a woman there in her car waiting to get in. We chatted a bit. She was an artist, from Canada, and was hoping to get in early because the lighting would be nice. She told me about her dogs (that were not with her) and her family. We say a few interesting critters from the levee road outside the gate including a mink. I did not get a picture of the mink alas. But I did get a pic of a hawk.

We saw some pickup trucks driving by that we hoped would be someone to open the gate but after 20 or so minutes I decided I wanted to go SOMEWHERE to go for a hike and was not going to wait for the key person. So I headed off to the Davis Wetlands. Not as much shade there and not really where I wanted to go. But I felt like it was the next best option.

On the drive in to the Wetlands I saw an otter family cross the road (no pics of them). But it seemed to be a good omen. I parked, got my stuff together and headed out for a walk. It was not about 7 AM. And it was already getting pretty warm. And lo and behold, just five minutes into the walk I got a nice sighting of a muskrat, swimming towards me.

And got a little video

And then continued on my walk and got to see some nice birds and got a few good pics of some including these:

My apple watch kept getting annoyed when I stopped to look at birds.

I took a few selfies too …

And on the way back I stopped by the spot where I had seen the muskrat and before I could get my camera ready I startled a beaver (no pics alas). And a few minutes later the muskrat came out.

And then I was off to my car to head home. But on the way out of the wetlands I also saw some deer.

Overall I would say that this was a pretty nice outing. More mammals than I was used to seeing in a day. Mink, otter, muskrat, beaver, and deer. Cool.

And then I headed home. But this was not the end of the story. Because just around sunset my wife said our daugther was a bit bored and had not gotten out all day and I asked if I might be able to take her out to do a quick shopping run. I said sure, espeically since I knew that my daughter was likely willing to do a little drive to look for wildlife afterwards. So we headed out, made a stop to do some quick shopping, and then I asked my daughter if she wanted to drive by the entrance of Yolo Bypass to see if we could catch the bats coming up form under the causeway. See a post I wrote about these bats from 2014 here: https://phylogenomics.me/2014/07/26/bat-tour-at-yolo-basin-wetlands/.

So we headed over to Yolo Bypass, with some trpidation because of the earlier locked gate. But now the gate was not locked although it was likely to be locked shortly since they close up at sunset. And it was just getting to be sunset. So we parked on the little levee road where I had parked in the morning, got out, and lo and behold got to see the bats flying out from the causeway. I made a short video and then my phone battery died so alas I did not make others. Here is that video. My phone makes it look lighter than it was out — it was actually quite dark.

And then when we had enough of the bats we decided to do a little drive around rural areas to see if we could see any wildlife. We do this often, although never before had we done this after sunset. And we did what we always do on drives. We guess what mammal species we might see. I chose opoosum. She chose coyote. And then changed her mind thinking that was too unlikely so she chose skunk. We drove around slowly on some rural roads and saw a lot of bunnies but no other mammals (we see so many bunnies and their relatives around here that we no longer allow them as one of the guesses).

And then on a rural road between Davis and Woodland we hit the jackpot. Juveniles coyotes. OMG. OMG. OMG.. They were so cutre. Got some videos and a few pics (with my cell phone – my real camera does not do well in low light). Actually fumbled quite a bit and missed a lot of the scene but at least caputred some of it. Here are some pics and videos.

We were SO excited about this. Just amazing to see these juvenile coyotes. And even though my daughter had originally picked coyote but then changed her pick to skunk, we both agreed she deserved credit for the original pick. And though we wanted to stay and see if the coyotes came back, we decided to head back home. And then a few minutes later we struck gold.

A mother and juvenile fox. I have never seen a fox around here. And these two were not exceptionally shy so we got good looks.

Made a few movies – the juvenile headed into the brush.

After the juvenile headed into the shrubs the adult stayed around and just sat there. So amazing.

What a day. It went from a possible disaster with Yolo Bypass being closed to a day where I saw a slew of mammals – a mink, two otters, a muskrat, a beaver, two deer, many bats, two juvenile coyotes and a juvenile and adult fox. Just amazing. And my daughter was beyond thrillled.

Article about Dr. Connie Rojas getting UC Davis Chancellor’s Postdoctoral Fellow Award

See Researcher Studying the Microbiome and Chemical Communication of Cats Named a Chancellor’s Postdoctoral Fellow for an article by Greg Watry about Dr. Connie Rojas who is a post-doc in my lab. Dr. Rojas got a UC Davis Chancellor’s Postdoctoral Fellow Award to come to UC Davis to work on cats and the role of their microbiome in chemical signaling and scent production.

For more about Dr. Rojas see

Twitter: @ConnieLaBiologa

Web Site: conniearojas.weebly.com