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

A kickstarter campaign to make a children’s book about evolution

Cool. A kickstarter campaign to make a children’s book about evolution.

  https://www.kickstarter.com/projects/breadpiginc/great-adaptations-a-childrens-book-about-evolution/widget/video.html

The Quest for a Field Guide to the Microbes: talk at "Science in the River City"

I got invited a while back to give a talk at a “Science in the River City” workshop for 3rd – 12th grade science teachers.  I proposed (and they said yes) to the idea of talking about my “Quest for A Field Guide to the Microbes.”  I recorded the screen (slides) and audio from my talk using Camtasia and have now posted the slideshow and slides.  Here they are:

Talk slideshow with Audio on Youtube:

 

 Slides on Slideshare

The start of a slow poop movement?

Well I am not 100% sure I believe all the claims in this but it is fascinating: What Drives a Sloth’s Ritualistic Trek to Poop? | Articles | Smithsonian.  I knew nothing about sloths and their poop until reading this.  The key part of the article to me:

The scientists’ results point to linked mutualisms between the sloths, the algae, and the moths: the sloth climbs down the tree to poop and, because the ground around the tree is littered with poop from previous descents, moth larvae growing in the poop can hitch a ride on the sloth’s back. The moths find shelter and thrive in the fur ecosystem. They also bring nutrients to their new home from the poop they were born in and when they die and decompose. Those nutrients fuel algae growth in the fur, and the algae supplement sloths’ foliage diets with lipids that the scientists speculate could serve as a high-energy snack. Then, when the sloths go down to do their business again, moths hop on their back and the cycle starts over again. 

I think this could be the start of a slow poop movement …

Carin Bondar video on "Organisms do Evolve" based on Miley Cyrus’ Wrecking Ball

I love Carin Bondar.

Compare to the original

Storify-based notes on #SMBE13 session on evolution of microbes and their genomes

Just finally getting notes up from the SMBE 2013 meeting session on “Diversity and evolution of microbes and their genomes” that I chaired.  After some issues with Storify I managed to record a “storification” with Twitter posts from the session. It is embedded below.

The talks were as follows:
Invited Talks

  • Holly Bik, UC Davis, Microbial Metazoa and the Taxonomic Abyss 
  • Lauras Katz, Smith College, Genome Dynamics across the Eukaryotic Tree of Life 
  • Jennifer Gardy, Of Snow and Short Reads: How Microbial Genomics Is Changing Public Health, British Columbia Center for Disease Control 
  • Tanja Woyke, Insights into the Phylogeny and Coding Potential of Microbial Dark Matter DOE Joint Genome Institute 

Talks selected from submitted abstracts

  • Pedro H. Oliveira: A Comparative Genomics Approach Provides New Insights into the Distribution and Evolutionary History of Restriction Modification Systems in Bacteria, Institut Pasteur 
  • Daniel J. Wilson, Genomic Insights into Within-Host Evolution and Pathogenesis in Staphylococcus aureus, University of Oxford 
  • John P. McCutcheon, Extensive Horizontal Gene Transfer Complements Missing Symbiont Genes in Mealybugs, U. Montana, 
  • Florent Lassalle, Biased Gene Conversion Shapes the Bacterial Genome Landscape, University of Lyon

New paper from some in the Eisen lab: phylogeny driven sequencing of cyanobacteria

(Cross post from my lab blog)

Quick post here.  This paper came out a few months ago but it was not freely available so I did not write about it (it is in PNAS but was not published with the PNAS Open Option — not my choice – lead author did not choose that option and I was not really in the loop when that choice was made).

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. [Proc Natl Acad Sci U S A. 2013] – PubMed – NCBI.
Anyway – it is now in Pubmed Central and at least freely available so I felt OK posting about it now.  It is in a way a follow up to the “A phylogeny driven genomic encyclopedia of bacteria and archaea” paper (AKA GEBA) from 2009 with this paper a zooming in on the cyanobacteria.

New paper from some in the Eisen lab: phylogeny driven sequencing of cyanobacteria

Quick post here.  This paper came out a few months ago but it was not freely available so I did not write about it (it is in PNAS but was not published with the PNAS Open Option — not my choice – lead author did not choose that option and I was not really in the loop when that choice was made).

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. [Proc Natl Acad Sci U S A. 2013] – PubMed – NCBI.

Anyway – it is now in Pubmed Central and at least freely available so I felt OK posting about it now.  It is in a way a follow up to the “A phylogeny driven genomic encyclopedia of bacteria and archaea” paper (AKA GEBA) from 2009 with this paper a zooming in on the cyanobacteria.

 

Twisted tree of life award #15: NBC News on "Junk DNA mystery"

Oh for fu$*# sake.  Really MSNBC?  I mean, I know perhaps I should not expect much from some in the press but this is just awful: ‘Junk’ DNA mystery solved: It’s not needed.

Brought to us by NBC News and LiveScience (which actually can have some pretty good science coverage).  This article has some complete and utter crap:

Some parts that I have issues with:

  • The headline: “‘Junk’ DNA mystery solved: It’s not needed.”  The headline is silly but alas it is consistent with what is in the article.
  • So-called junk DNA, the vast majority of the genome that doesn’t code for proteins“.  So – they have redefined junk DNA as all non coding DNA?
  • “For decades, scientists have known that the vast majority of the genome is made up of DNA that doesn’t seem to contain genes or turn genes on or off.”  Apparently there is an entity out there known as “The Genome”.  
And then we get into the quoting of author and researcher Victor Albert with no comments or responses from anyone is painful too.
  • At least for a plant, junk DNA really is just junk — it’s not required.”  Except that they did not show this – they just showed that one plant can have a small genome and not have a lot of “junk” as they call it, which of course does not really say anything about what “junk” does or does not do in other organisms.
  • Nobody’s really known what junk DNA does or doesn’t do” apparently calling into question the some 10,000 plus papers on the topic.

Apparently, from reading the rest the whole point of this article is that it turns out that people sequenced the genome of a bladderwort and it has a small genome but a lot of genes.  Oh and the organism is complex.  Therefore, apparently, it follows that

“The findings suggest junk DNA really isn’t needed for healthy plants — and that may also hold for other organisms, such as humans.”

And this leads us to ‘Junk’ DNA mystery solved: It’s not needed.

So – basically – if ONE FUCKING ORGANISM DELETES SOME OF IT’S NON PROTEIN CODING PORTIONS OF ITS GENOME THEN THIS MEANS THAT ALL NON CODING DNA IS USELESS.

Aaaaaaaaaaaaaaaaaaargh.

And for this evolutionary logic, I am awarding NBC News, Tia Ghose (the author of the piece) and Victor Albert, the 15th coveted Twisted Tree of Life Award.

Past winners:
UPDATE 5/17/13
Some other discussions of this paper and related to my critique (though not always agreeing with me)

APRIL WORKSHOP: Phylogenetically correct stats for evolutionary ecologists (RSVP needed)

From CPB Postdoc Luke Mahler:

Dear Davis Ecologists and Evolutionary Biologists,

This Spring Quarter, I’ll be delivering my CPB Postdoctoral Fellowship Workshop, which will be entitled:

“Phylogenetically correct analysis of species data in ecology and evolution”.

This workshop will consist of 3 sessions, to take place over three days:

April 2: 4:10PM-5:30PM (lecture; note this will be the CPB seminar for this week)
April 3: 11:00AM-1:00PM (tutorial 1 – feel free to bring your lunch)
April 4: 1:00PM-3:00PM (tutorial 2)

The format of this workshop will be an introductory lecture followed by two hands-on R tutorials.

In the lecture, which will take place during that week’s CPB seminar slot, my goal is to (1) review why it’s important to account for phylogeny during data analysis, (2) briefly introduce a suite of current methods for doing so, and (3) critically discuss the inherent assumptions and limitations of phylogenetic comparative methods, outlining best practices for conducting basic analyses.

In tutorials, I will lead participants in a series of computer exercises (all in R) designed to provide hands-on experience implementing the most commonly used phylogenetic statistical analyses. In the first tutorial, participants will learn how to prepare and import phylogenetic trees and species data set for analysis, how to visually explore these data, and how to measure phylogenetic signal and select an appropriate model of trait evolution. In the second tutorial, we’ll conduct a number of phylogenetic statistical analyses with a focus on linear models and principal component analysis. We’ll discuss parameter estimation and interpretation under these models, and will cover techniques for assessing sensitivity of results to phylogenetic uncertainty.

The target audience for this workshop are scientists at any stage who are familiar with phylogenetic trees but don’t necessarily have specialized knowledge about how to work with trees when analyzing ecological or other comparative data. No prior experience using R is necessary, although attendees will need to bring their own laptops, and will need to install R in advance of the workshop (it’s free). Attendees do not need to bring data files – we’ll analyze example data sets which I will provide. Faculty, postdocs, and students are all welcome to attend.

If you are interested in attending this workshop, PLEASE CONTACT ME BY EMAILING lmahler@ucdavis.edu. We haven’t decided yet where to hold the workshop – this decision will be based on anticipated attendance. We’ll do our best to secure a room that can accommodate everyone who interested in attending, but can’t guarantee there will be room for you if you don’t let me know in advance.

Thanks, and I hope you can make it.

Best,
Luke Mahler

Center for Population Biology Postdoctoral Fellow
2320 Storer Hall
University of California, Davis
One Shields Avenue
Davis, CA 95616, USA