23Apr / 2022

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

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23Apr / 2014

A special special issue of RNA Biology – dedicated to Carl Woese and Open Access too

A must read for, well, everyone out there: RNA Biology: Table of Contents for a special issue dedicated to / about Carl Woese. The issue includes an amazing collection of papers:

A special issue in memoriam of Carl Woese

Renée Schroeder

Page 169

http://dx.doi.org/10.4161/rna.28566

Introduction to special Carl Woese issue in RNA Biology

Robin R Gutell

Pages 170 - 171

http://dx.doi.org/10.4161/rna.28393

Carl Woese: A structural biologist’s perspective

Peter B Moore

Pages 172 - 174

http://dx.doi.org/10.4161/rna.27428

Early days with Carl

Ralph Wolfe

Page 175

http://dx.doi.org/10.4161/rna.27429

Molecular phylogenetics before sequences: Oligonucleotide catalogs as k-mer spectra

Mark A Ragan, Guillaume Bernard and Cheong Xin Chan

Pages 176 - 185

http://dx.doi.org/10.4161/rna.27505

Constraint and opportunity in genome innovation

James A Shapiro

Pages 186 - 196

http://dx.doi.org/10.4161/rna.27506

Carl Woese's vision of cellular evolution and the domains of life

Eugene V Koonin

Pages 197 - 204

http://dx.doi.org/10.4161/rna.27673

From Woese to Wired: The unexpected payoffs of basic research

Ann Reid

Pages 205 - 206

http://dx.doi.org/10.4161/rna.27701

Carl Woese, Dick Young, and the roots of astrobiology

John D Rummel

Pages 207 - 209

http://dx.doi.org/10.4161/rna.27702

Life is translation

Bojan Zagrovic

Pages 210 - 212

http://dx.doi.org/10.4161/rna.27718

Organelle evolution, fragmented rRNAs, and Carl

Michael W Gray

Pages 213 - 216

http://dx.doi.org/10.4161/rna.27799

Remembering Carl Woese

Kenneth R Luehrsen

Pages 217 - 219

http://dx.doi.org/10.4161/rna.27800

Woese on the received view of evolution

Sahotra Sarkar

Pages 220 - 224

http://dx.doi.org/10.4161/rna.27883

This article is open accessSecondary structure adventures with Carl Woese

Harry F Noller

Pages 225 - 231

http://dx.doi.org/10.4161/rna.27970

A backward view from 16S rRNA to archaea to the universal tree of life to progenotes: Reminiscences of Carl Woese

Roger A Garrett

Pages 232 - 235

http://dx.doi.org/10.4161/rna.28228

Carl Woese in Schenectady: The forgotten years

Larry Gold

Pages 236 - 238

http://dx.doi.org/10.4161/rna.28305

History and impact of RDP: A legacy from Carl Woese to microbiology

James R Cole and James M Tiedje

Pages 239 - 243

http://dx.doi.org/10.4161/rna.28306

Casting a long shadow in the classroom: An educator’s perspective of the contributions of Carl Woese

Mark Martin

Pages 244 - 247

http://dx.doi.org/10.4161/rna.28002

Looking in the right direction: Carl Woese and evolutionary biology

Nigel Goldenfeld

Pages 248 - 253

http://dx.doi.org/10.4161/rna.28640

Ten lessons with Carl Woese about RNA and comparative analysis

Robin R Gutell

Pages 254 - 272

http://dx.doi.org/10.4161/rna.28718

Memories of Carl from an improbable friend

Harris A Lewin

Pages 273 - 278

http://dx.doi.org/10.4161/rna.28866

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10Oct / 2013

Rob Desalle Talk at UC Davis – Storification of Twitter Notes

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14Feb / 2013

Meet the Texas Blind Salamander

The Texas Blind Salamander (Eurycea rathbuni) is a cave salamander that has adapted to life living in the dark. With extremely underdeveloped eyes, unpigmented skin, and the retention of its juvenile aquatic form, this salamander is perfectly suited to live in the underground cave streams. Found only in caves around San Marcos, Texas these salamanders are actually considered endangered on the State level. Because they live only in specific areas and rely on the Edwards aquifer, the Texas blind salamander is extremely susceptible to changes in water quality. Their size reaches between 3 and 5 inches and they eat a diet of most aquatic invertebrates.

Click here to read this story about a day in the life of the Texas Blind Salamander from the Tree of Life project.

Watch this video to see Eurycea rathbuni doing his thing at the Edwards aquifer:

Stay tuned to Nature Afield tomorrow for a follow-up on the interesting mating habits of the Texas Blind Salamander!!!

“Meet the…” is a collaboration between The Finch & Pea and Nature Afield to bring Nature’s amazing creatures into your home.

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31Dec / 2012

RIP Carl Woese: Collecting posts / notes / other information about my main science hero here

My tribute to Carl Woese 12/30/12

Sadly, Carl Woese has passed away. I am collecting some links and posts about him here in his memory. He was without a doubt the person who most influenced my career as a scientist.

News stories about Woese's passing

Some of my posts about Woese

Woese Tree of Life pumpkin (by J. Eisen)

Storification of Tweets and other posts about his passing

Other posts worth reading about Woese's passing

Some videos with Woese

Miscellaneous

My graduate student Russell Neches used a laser to etch a picture of Carl Woese on a piece of toast.

More about Carl Woese

Papers by Carl Woese is a group in Biological Sciences on Mendeley.

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12Nov / 2012

Linkonomicon IX

How to flip food like a chef

Chef Ben taught me this years ago, but h/t goes to Laughing Squid

Nate Silver, the Accuratest?

‘Pale Blue Dot’ animated

via Maria Popova at Brain Pickings

Fractal inspired Tree of Life

Rock Out like a Flapper to 1920s Jazz

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13Sep / 2012

Some quick comments on "Giant viruses coexisted w/ the cellular ancestors & represent a distinct supergroup"

Got asked on Twitter about this paper:

BMC Evolutionary Biology | Abstract | Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya

Hmm... @carlzimmer @phylogenomics? Weigh in?RT @diana_yates_: Study of giant viruses shakes up the tree of life:bit.ly/NqLX2u
— Ed Yong(@edyong209) September 13, 2012

I answered briefly

@edyong209 @carlzimmer @diana_yates_ very unconvincing; no taxa in trees; no evidence FSF useful marker; Fig 3 strange; data not released ..
— Jonathan Eisen (@phylogenomics) September 13, 2012

Don't have time for a detailed blog post but here are some quick comments:

1. Giant viruses are fascinating and cool

2. I have done work connected to the topic of this paper and thus might not be considered fully objective. For example see

3. I see no evidence that the type of analysis that they do on protein folds is a robust phylogenetic method. Phylogeny from sequence alignments (which is what we focus on in my lab) have been tested and tweaked for some 50 years. There are 100s to maybe 1000s of papers on methods alone - not to mention the 1000s of papers using alignments for phylogenetics. I am not convinced that the analysis being done here of FFs and FSFs is particularly robust. It seems interesting, certainly. But is it sound? I mean, I could build phylogenetic trees from cell size, from shape, from eye color, and from all sorts of other features. Those would all suck for certain. Protein folds - not sure about them. They almost certainly are prone to convergent evolution and I do not see any attempt in this analysis to deal with that issue.

4. The authors of the current paper do not show any taxa names on their trees - just colors for large groups of taxa (bacteria, archaea, eukaryotes and viruses). It is really not good practice to remove the taxon names. If they were there the first thing I would do is to look at the patterns within the groups they highlight. Do all the major phyla / kingdoms of eukaryotes, for example, come out looking as one would expect based upon other studies. Or are they all over the place? Same for bacteria and archaea. Not including taxa makes it nearly impossible to judge this paper positively. I could not find this information in supplemental data either.

5. They really should have released the data tables they used for the phylogenetic analysis. Don't know why they did not.

6. In Figure 3 with the rooting they have, either viruses are a subgroup of archaea or archaea are not monophyletic. Not a good thing in a paper trying to claim viruses represent a fourth grouping on the tree of life.

Anyway - got to do some other things but just wanted to get some comments out there.

UPDATE 9/19 - some prior stories about the "fourth domain" and ancient viruses - to counter notion in the press release for this paper that their findings "shake up the tree of life". Even if their specific inferences about viral evolution are correct, such inferences / conclusions have been made before.