Tag: Evolution

A distasteful & disgraceful "Are there limits to evolution?" meeting at the University of Cambridge #YAMMM

Well, I saw this Tweet the other day

//platform.twitter.com/widgets.js And though there was a bit of a discussion on Twitter I felt I had to follow up with a blog post. When I saw the post I was at a conference (Lake Arrowhead Microbial Genomes) where I could get Twitter access but for some reason very little web access. So I could not dig around until now (I am home). 

This meeting is a complete disgrace and an embarassment for the field of evolutionary biology, for the University of Cambridge which is hosting the meeting, and for the Templeton Foundation which is sponsoring it.

Why do I say this? Well, pretty simple actually. The meeting site lists the Invited Keynote speakers for the meeting.  Notice anything?  How about I help you by bringing all the pictures together.

Notice anything now?  How about I help you some more by masking out the men and not the women.

Impressive no?  25 speakers – 23 of them male.  I guess that means there are no qualified female speakers who coudl discuss something about evolution right?  It would be worth reading “Fewer invited talks bu women in evolutionary biology symposia” to get some context.  What an incredible, disgusting, distasteful and disgraceful meeting.  
I recommend to everyone who was considering going to this meeting – skip it.  Also consider writing to the University of Cambirdge and the Templeton Foundation to express your thoughts about the meeting.  This certainly is a fine example of Yet Another Mostly Male Meeting (YAMMM).  Well, maybe I should word that differently – this is a disgusting example of a YAMMM.  

For more on this and related issues

  • Posts on Women in STEM


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    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    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

    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    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

    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    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

    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    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 …

    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

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

    I love Carin Bondar.

    Compare to the original

    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    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
    //storify.com/phylogenomics/smbe-2013-session-on-microbial-genome-evolution/embed//storify.com/phylogenomics/smbe-2013-session-on-microbial-genome-evolution.js[View the story “SMBE 2013 session on microbial genome evolution” on Storify]

    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    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.
    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    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)
    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–