Jonathan A. Eisen | Lightnews

Jonathan Eisen

@phylogenomics.bsky.social

31K followers 5.5K following 2.1K posts

Prof at #UCDavis

Work: evolution, ecology, function & phylogenomics of host-microbiome systems; #openscience;
Other: #birds; baseball; T1D

Lab phylogenomics.me
Pics jonathaneisen.smugmug.com
Links linktr.ee/jonathaneisen
TED go.ted.com/6WPm .. more

Videos

Jonathan Andrew Eisen is an American evolutionary biologist, currently working at University of California, Davis. His academic research is in the fields of evolutionary biology, genomics and microbiology and he is the academic editor-in-chief of the open access journal PLOS Biology. .. more

Biology 43%

Environmental science 24%

Posts Replies Media Videos

Pinned

Jonathan Eisen @phylogenomics.bsky.social · Aug 31

Gratitude. Just made a little video while out for a walk on my birthday to express my gratitude to all the people and organizations that help protect and preserve the natural world and make it accessible. Thanks to all of you. #gratitude #nature #birds #hiking #birthday #california #yolobypass

Jonathan Eisen @phylogenomics.bsky.social · 41m

And he would drive me there in this gigantic old American can he had (somelike like a Pontiac Grand Prix). It was like I entered a time warp or something - discussion papers from the 1950s on DNA metabolism and such while driving around in this bomber .. 8/n

Jonathan Eisen @phylogenomics.bsky.social · 41m

One of my favorite memories of Ham from when I worked at TIGR is that he liked to pick my brain about DNA repair and evolution so once every 2-3 months or so he would take me out to lunch at a Chinese Restaurant in Rockville 7/n

Reposted by Jonathan A. Eisen

Alex Merz 🇺🇸🇨🇦🇺🇦 @merz.bsky.social · 42m

Ham Smith and JCV's sequencing of H. flu' was a watershed moment for me as well. I was in grad school and, looking at the first annotated gene list, I realized that I knew at least crudely what maybe half of the proteins in *an entire organism* were doing. that notion of comprehensibility was 🤯.

Jonathan Eisen @phylogenomics.bsky.social · 51m

And without a doubt that talk was one of the most influential moments of my life and career. I will miss him and always remember him. 6/n

Jonathan Eisen @phylogenomics.bsky.social · 51m

This eventually led to finagling my way into a dinner w/ Craig Venter a few years later, and this let to a job at TIGR. And thankfully, I got to know and work with Ham Smith during and after my time there. What a wonderful person and brilliant scientist. 5/n

Jonathan Eisen @phylogenomics.bsky.social · 51m

And many of the organisms I was trying to pull out single genes from were on the list (e.g., Deinococcus radiodurans, Aquifex, Pyrococcus, ...). So, talked to Ham after his talk, confirmed the details of the list, and dropped PCR and shifted to a focus on analyzing genomes 4/n

Jonathan Eisen @phylogenomics.bsky.social · 51m

It was what Ham Smith showed later in this talk that let me to dump my PCRs and become a genomic scientist. He showed a list of genomes being sequenced by TIGR and other places (I wrote some but not all down in my notes). 3/n

Jonathan Eisen @phylogenomics.bsky.social · 51m

The whole concept of sequencing whole genomes of organisms using the "shotgun" method was amazing. At the time I was trying to clone out individual DNA repair genes from various weird organisms using degenerate PCR 2/n

Jonathan Eisen @phylogenomics.bsky.social · 51m

When I was in graduate school my life and carreer were completely transformed by a seminar I attended at Stanford by Dr. Hamilton Smith. In the talk he discussed how TIGR was sequencing whole genomes of organisms. Here is a scan of P1 of my notes. 1/n

Reposted by Jonathan A. Eisen

Brett Baker @archaeal.bsky.social · 13h

Did someone say Asgard?

www.biorxiv.org/content/10.1...

www.biorxiv.org/content/10.1...

An Asgard archaeon with internal membrane compartments

The emergence of eukaryotes from a merger between an archaeon and a bacterial cell ∼two billion years ago involved a profound change in cellular organisation. While the order in which different featur...

www.biorxiv.org

Jonathan Eisen @phylogenomics.bsky.social · 1d

Football was good to watch today because the teams I was rooting for never gave up. Alas can’t say that for another team I root for.

Reposted by Jonathan A. Eisen

Dr. Orchid @ohwellokay.bsky.social · 2d

Ah, but you forgot: personally off-putting and unpleasant

Reposted by Jonathan A. Eisen, James M. Bullock, Brian Keegan

Lior Pachter @lpachter.bsky.social · 3d

Scientific breakthroughs are rarely unique; someone else would’ve made them soon enough. But when prominent scientists cause harm, that harm isn’t inevitable; the world might simply have been better had the harm not been inflicted.
liorpachter.wordpress.com/2018/05/18/j...

James Watson in his own words

“Some anti-Semitism is justified” “Whenever you interview fat people, you feel bad, because you know you’re not going to hire them” “Japan should be bombed for d…

liorpachter.wordpress.com

Jonathan Eisen @phylogenomics.bsky.social · 3d

So - sure - he had lots of impact on science and society. But I wrote the 1st comments here because, well, he was pretty vile in many many ways. And my personal experiences with him were mostly negative ...

Jonathan Eisen @phylogenomics.bsky.social · 3d

After one particularly egregious set of comments by Watson about blacks and Jews, I and the other authors got legal advice on how to add wording to our contract that would make sure Watson would not be able to insert any deranged ideas into our book

Jonathan Eisen @phylogenomics.bsky.social · 3d

Meeting with him was always, well, interesting. Sometimes it was fun. But most of the time, it was disturbing because he would go on and on about some idea he had connected to evolution or genomics that was racist or sexist or, usually, both.

Jonathan Eisen @phylogenomics.bsky.social · 3d

On many of those visits I (and many of the other authors) met with Jim Watson and sometimes had dinners with him, as he had played a role in getting the book off the ground.

Jonathan Eisen @phylogenomics.bsky.social · 3d

Story: Many years ago, every few months over a period of 5+ years, I would head up to Cold Spring Harbor Labs to work on an Evolution textbook (see cshlpress.com/default.tpl?...).

cshlpress.com

Reposted by Jonathan A. Eisen

Goldie and Komos @komos-and-goldie.bsky.social · 3d

He also thought women should be genetically engineered to make them all sexier. Just an utterly jaw-dropping thing for someone who lived through WWII to say.

Reposted by Jonathan A. Eisen

Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 3d

Homophobic too.

Jonathan Eisen @phylogenomics.bsky.social · 3d

Sorry - all out of nuance for the day ...

Reposted by Jonathan A. Eisen

John Wallach @jmwallach.bsky.social · 3d

But he was also an asshole.

Reposted by Anne Hilborn

Jonathan Eisen @phylogenomics.bsky.social · 3d

Yes, some people's legacies are complicated. For example, Watson. After all, though he was racist, don't forget his other traits. For example, he was also sexist. And also anti-semitic. And a data / idea thief. So let's not forget all the different facets.

Jonathan Eisen @phylogenomics.bsky.social · 3d

Thanks

Jonathan Eisen @phylogenomics.bsky.social · 3d

thanks

Jonathan Eisen @phylogenomics.bsky.social · 3d

My last A1C was 6.1 which is pretty good. It has fluctuated by been trying crazy hard to keep my blood sugar levels in a reasonable range ... and seems likely that this has helped limit complications.

Jonathan Eisen @phylogenomics.bsky.social · 3d

Well, type 1 diabetes for > 40 years has taken a toll, but I have worked very hard to stay in control and limit complications. And today I got some good news. My eyes are basically fine. Kind of stunned since in the past I had some issues. #type1 #agoodday

Reposted by Jonathan A. Eisen, Rafael Candido‐Ribeiro

Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 3d

¿Hiciste tu doctorado en México? ¿Quieres hacer un postdoc en California? ¿Te interesa la genética evolutiva? ¡Checa esta beca y mándame un mensaje! alianzamx.universityofcalifornia.edu/research-and...

Postdoctoral Research Fellowships - University of California Alianza MX

Submitting an Application Current Fellows 2025 Cohort Additional Information Humberger Toggle Menu Interested in applying for a Postdoctoral Research Fellowship? Eligibility The program seeks applican...

alianzamx.universityofcalifornia.edu

Reposted by Jonathan A. Eisen, Axel Bruns, Kelly R. Zamudio , and 9 more Jonathan A. Eisen, Axel Bruns, Kelly R. Zamudio, John McLaren, Smith, Jérôme Denis, Rebecca Tushnet, Carlos Nunes Silva, Stacy D. VanDeveer, Els Torreele, Pieter Vantieghem, Anne Hilborn

Terry McGlynn @hormiga.bsky.social · 3d

Hey folks, as news of Watson's demise spreads, please don't set aside his weighty legacy of misogyny and racism. He was truly among the worst of us. www.vox.com/2019/1/15/18...

DNA scientist James Watson has a remarkably long history of sexist, racist public comments

“People say it would be terrible if we made all girls pretty,” he said in 2003. “I think it would be great.”

www.vox.com

Reposted by Jonathan A. Eisen

Mark Mandel @markjmandel.bsky.social · 3d

Great profile of @ruthlessruth15.bsky.social www.the-scientist.com/postdoc-port...

Postdoc Portrait: Ruth Isenberg

This postdoc explores how gut and oral bacteria wage microscopic battles that shape infection and health.

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