Eisen Lab Blog

No need to oversell the human microbiome with studies like these …

I know I complain all the time about news stories and people “overselling the microbiome“.  Mind you, I believe microbial communities are likely to be found to have very very important roles in the biology of the plants and animals and other organisms on which they live, but I worry about overhyping the possibilities.  But thankfully, there are some good researchers at work out there documenting just what the microbiome can and does do.  And the results continue to be promising.

Here is the one that caught my eye most recently: BBC News – ‘Weight loss gut bacterium’ found about this PNAS paper.  While the study is in mice and it is what one could call “limited” in some ways, it is really fascinating and has much promise.  Basically, they isolated a new bacterium (with the awkward name of Akkermansia muciniphila, and did a series of experiments in mice looking at the role this bacterium can play in many mouse gut properties.  But most interesting, treatment of mice with this bacterium (and only when the bacterium was alive) led to a reduction in high fat induced metabolic disorders and obesity.  I am still re-reading the paper but the result seems solid.  And exciting.

So – there is no need to oversell the microbiome when the results coming in sell themselves …

UPDATE 30 minutes after posting

Of course, I should have checked to see if Ed Yong wrote anything about this.  And he did: The Mucus-Lover that Stops Mice from Getting Fat.  Read his post.  It is excellent.  With ALL sorts of links and background and other detail.

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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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Aquarium 16S library submitted today

Seven months after starting the sample collections we finally submitted our pooled 16S library today for sequencing.  We have somewhere around 90 samples from a few different types of aquariums and our community succession experiment.  Now time for everyone to learn QIIME!

 

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.

——–

Two more papers out: Jessica and Amanda

The days of this blog are numbered…  There’s only a couple more papers to come out (both accepted) and then this project will be officially completed!   I’ll write a summary and reflections on the whole process at that time.

Meanwhile, congrats to Jessica and Amanda whose papers came out this week:

Jessica’s Kocuria paper

Amanda’s Dietzia paper

Sitting in the lab

I’m sitting here in the lab looking at our google doc and it’s looking pretty good! We only have a few final dilutions to do and we’ll be on our way to sequencing! I’m waiting for David to come back from lunch so he can update me on the next steps.

 

I’m excited for what’s to come!

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.
——–
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.

——–

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.

——–

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 …
——–
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.

——–

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