Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

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)
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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.

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Crosspost: Woohoo – two more genome announcement papers from our undergraduate project on built environment reference genomes

Crossposting this from the microBEnet blog.
Two new papers out from the microBEnet Undergraduate Research: Built Environment Reference Genomes  project:
These go with two previously published ones:
And two more coming. So proud of the undergrads in my lab who did this work and David Coil for coordinating it with help from Jenna Lang and Aaron Darling.  Undergrads at UC Davis sequencing genomes of organisms they isolated. So cool.
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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.

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YAMMGM: Yet another mostly male genomics meeting #2: Beyond the Genome 2013

Well, the “winner” of this months YAMMGM award is Beyond the Genome 2013 | Mission Bay | San Francisco

Alas, YAMMGM stands for “Yet another mostly male genomics meeting” so it is not an award to covet.

This meetings listed speakers are below with women highlighted in green.

  • Nicholas Navin -The University of Texas MD Anderson Cancer Center
  • Sunney Xie – Harvard
  • Xu Xun – BGI
  • James Hicks -CSHL
  • Fuchou Tang – Peking
  • Itai Yanai – Israel
  • Thierry Voet – Sanger
  • Jacob Kitzman – Plasma cell free DNA sequencing
  • Stephen Quake – Stanford and Fluidigm
  • Mario Caccamo – Genome Analysis Centre
  • Rob Martienssen – CSHL
  • Ryan Lister – University of Westerm Australia
  • Neelima Sinha – UC davis
  • Jorge Dubcovsky – UC Davis
  • Robert Schmitz (Salk) – 1001 Arabidopsis project and CHiP-Seq
  • Marja Timmermans (CSHL)
  • Magnus Nordborg
  • Chairs Alicia Oshlack, Yingrui Li and Michael Schatz to chair the bioinformatics challenge.
  • James Taylor – Emory and Galaxy
  • Chris Dagdigian – Bioteam
  • David Haussler -UC Santa Cruz
  • Janet Kelso – Max Planck Institute for Evolutionary Anthropology

That comes to 16.6% if you count all listed.  If you exclude session chairs the numbers are a little different but still pretty low.

Certainly this does not prove any bias on the part of the meeting organizers.  But it certainly suggests to me they might want to think about why the ratio is skewed.

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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.

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A good thing: More and more biology papers showing up in arXiv

Good to see some more papers in microbiology & genomics and related topics going to the preprint server arXiv.

If you are interested in population and evolutionary genetics a good place to keep up with papers on this topic in arXiv is Haldane’s Sieve.  The good folks there in essence make a separate post about each paper of interest and then people can comment there on the papers, since the commenting functions at arXiv are, well, challenged.

In areas related to this blog, here are some recent papers in arXiv:

Am hoping more and more biologists start depositing papers in arXiv.  My brother has started doing it for all papers in his lab so I guess that means I should too.  And so should everyone else …
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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.

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Media & STEM Research:5/31:12-2pm at #UCDavis

STEMSocialMediaDiscussionLunch_flyer_2.pdf

10AM at #UCDavis – David Botstein “Coordination of growth rates, stress response & metabolic activity in yeast”

Special Seminar

Department of Microbiology and Molecular Genetics

*Note the special time and day

Dr. David Botstein
(Anthony B. Evnin Professor of Genomics)

"Coordination of Growth Rate, Stress Response and Metabolic Activity in Yeast"

Tuesday, May 7, 2013

10:00 am

1022 Life Sciences

Botstein 5-7-13.doc

The need for a phylogeny driven genomic encyclopedia of eukaryotes

Monday I gave a talk for the SMBE Eukaryotic Omics satellite meeting that has been going on at UC Davis.  When Holly Bik, a post doc in my lab asked me to talk at the meeting, I said, basically “Well, OK, but I don’t really do much work on eukaryotes.”  And then I came up with an idea – I could make my talk about how it might be good to have a better phylogenetic sampling of eukaryotic genome sequences.  I have been a bit obsessed for many many years about phylogenetic sampling of genomes and, well, though I have avoided eukaryotes mostly in most of my genome sequencing work, I figured, I should still get on my soap box about how phylogenetic sampling is a good thing.  So, well, I did.  And I think we (i.e., the scientific community) really needs a better sampling of eukaryotic genomes.

I have posted my talk to Slideshare and I recorded audio of my talk in synch with the slides and posted that to Youtube.  These are below.

I hereby am calling for those people interested in participating in such a phylogeny driven genomic encyclopedia of eukaryotes to make yourselves known.  We NEED to do this.

Related posts

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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.

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I love this … "Dr. Eleanor’s Book of Common Ants" based in part on citizen science data

This is really cool:  Dr. Eleanor’s Book of Common Ants.  Free to download.  With incredible pics from Alex Wild.  And based in part on data from the School of Ants citizen science project.  You can download the PDF or the iBook from iTunes.  From the folks at “Your Wild Life” including Holly Menninger and Rob Dunn and others.  Definitely worth checking out.

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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.

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New papers from people in the lab …

A lot of new papers from people in the lab in the last month or so.  See below for details of some of them:

Yes, the human microbiome has truly arrived: on Wait Wait Don’t Tell Me

So cool.  Yesterday on “wait wait … don’t tell me” Kai Penn (actor) was enticed to play the game “Ahhh! Get It Off Me!” in regard to microbes: Not My Job: Kal Penn Takes A Quiz On The Microbiome : NPR

Hat tip to Jenna Lang for pointing me to this.

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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.

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