Category: Misc.

Hey Nature Publishing Group – When are you going to live up to your promises about "free" genome papers? #opengate #aaaaaarrgh

This is just ridiculous.  Nature Publishing Group in 2007 announced that they were making all papers in their journals that reported genome sequences would be made freely available and would be given a Creative Commons license: Shared genomes : Article : Nature.

About a year ago I posted to twitter (using the hashtag #opengate) and my blog about how Nature Publishing Group was not following through on their promises.  See for example

and more including some from others
Amazingly, and pleasantly, I note, in my complaining I exacted some responses from people from Nature Publishing Group who swore that these were just oversights and they would fix them.  Well, alas, the money collecting machine of Nature Publishing Group is back.
For example, currently the following papers are not freely available even though at one point they were or they clearly fit in the “Shared genomes” definition Nature Publishing Group so happily promotes:
These above are all papers of mine, so I noticed them first (I noticed this when trying to create a Pintarest Baord for all my papers and not being able to get to a free page for these papers meant I couldn’t add them to the Board.  Could it be that Nature Publishing Group is just trying to get my goat?  Let’s see.  A brief search found these papers by others – all also not freely available even though all clearly fit Nature’s own definition of genome sequencing papers:
Here are some others

I think the funniest (and scariest) part may be the corrections and errata that are not freely available. And these are just the articles I found in a 15 minute search. I am sure there are more.  Yes, Nature Publishing Group has made many genome papers freely available.  That is great.  Much better than many other publishers.  But the cracks in your system are large and suggest that nobody there is actually dedicated to seeing through on the promises.  Promises are meaningless.  Follow through is the key.  Come on Nature Publishing Group – how about assigning a “Free access ombudsman” or something like that who will make sure that free means free.  I am sick of writing these posts.  You should do your own QC …

UPDATE: see some more recent blog posts of mine about this topic:

UPDATE 3-28-12 1 PM PST:
Well, if you look at the comments, Nature is apparently trying to fix this and most of the articles I listed above are now freely available (the corrections are still not free but they claim to be working on it).  But a simple search of Nature finds there are still some papers that are closed off that shouldn’t be:

It’s not that hard to find these.  It baffles me a bit how people at Nature don’t seem to be able to find them.  But maybe I am just really good at searching …

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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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12 hours of me: Slideshows w/ audio from "BIS2C: Biodiversity & the Tree of Life" at #UCDavis

Well, it has taken a few months of processing but I have finally gotten my lectures from the introductory biology course I teach uploaded in some way to share.  The course is “BIS2C: Biodiversity and the Tree of Life” and it is the third quarter of a three quarter introductory biology series at UC Davis.  Each year some 2300 or so students take this series which means that we at UC Davis have to offer each of the courses (BIS2A, BIS2B, and BIS2C) each quarter.   Every fall I co-teach BIS2C.  Alas we do not have a lecture hall big enough for 700 students, so we do the course in two sections.  The way we teach it each of the faculty double up and teach their part of the course to each section.  The course also has a weekly lab.  It is a machine of sorts.

This fall I taught 13 lectures for the course.  I covered basically phylogenetic methods, the big picture of the tree of life, and microbial diversity.  I used the Apple presentation program Keynote for slides for my lectures and I used the “Record Slideshow” option to record audio in synch with the slides.  After a bit of pain, I managed to convert these recordings into video and then posted them to Youtube.  And today I am sharing them with you.  There are imperfections of course.  But I thought some might find them useful.  Plus I have made a YouTube playlist for all the lectures if you want to just sit down and enjoy 12 hours or so of me.  Now if only Youtube would allow me to change the thumbnail image for each lecture …  Plus I note – next year I will be doing much more interactive learning in class so this may be the last record of some of these lectures …

Lecture 1: Introduction to Course and the Tree of Life

Lecture 2: Trees, Taxa and Groups

Lecture 3: Characters

Lecture 4: Phylogenetic Inference

Lecture 5: Phylogenetic Inference

Lecture 6: The Tree of Life

Lecture 7: The Three Domains

Lecture 8: Three Domains and Microbial Diversity

Lecture 9: Microbial Diversity

Lecture 10: Endosymbioses and Lateral Gene Transfer

Lecture 11: Endosymbioses and Lateral Gene Transfer

Lecture 12: Extremophiles

Lecture 13: Human Associated Microbes

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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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Just grand -Donald Williamson published more crap on larval "evolution" – this time in one of the #OMICS journals

Well this is great.  Just great.  Donald Williamson has a new paper “The Origins of Chordate Larvae” published in Cell and Developmental Biology – a spammy journal from the OMICS publishing group.  Don’t know who Williamson is?  Well consider yourself lucky.  For more on him and his horrendous history of publishing crap see:

And many many more.  Short summary – he has a theory regarding larval forms of organisms having a separate evolutionary history from adult forms.  He has no evidence for this.  And he keeps finding new ways to publish his theory.  Uggh.  I guess this serves as a reminder to everyone out there – crap does get published.  It is too bad.  But it does happen and will continue to.  We need to call out the crap as much as possible so that as few people as possible out there end up getting deceived.  So this is my contribution to that notion.  Google search engines pay attention. Donald Williamson really publishes some horrible stuff.
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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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Calling all computational biologists – do as C. Titus Brown does – submit your pubs to arXiv

Can I just express my love/respect for C. Titus Brown?  Not only is he into openness in science and metagenomics and such.  But he practices what he preaches.  For example see – Daily Life in an Ivory Basement : /mar-12/diginorm-paper-posted in which he describes his new submission to arXiv and some background.  I know I am big on Open Access and all, but even we have been lame about submitting things to preprint servers like arXiv.  Gonne do my best to fix that and try and copy Titus.

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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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Lenses in Biology collection from Nature Outlook: free (for now at least) & worth a look

Some nice long features in Nature Outlook on various topics plus interviews with the authors.  Summed up in Lenses on Biology.  All freely available though I think that is only for this collection and not in general for Nature Outlook.

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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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Notes (from me and mostly others) from the JGI User Meeting #JGIUM7

OK, so the DOE Joint Genome Institute User Meeting is underway. Day 2 just finished. And I have been there for much of it but alas, not in some of the talks since I can’t seem to get past the hallway/gathering area outside the talks. There are way way too many people there who I have not talked to or seen in a while … So … apologies to those who thought I might be live tweeting the whole meeting … it just hasn’t happened. But I did use the Storify web tool to make a “storification” of posts to twitter from the meeting – most of which were from other people. Here is the story in slideshow format.

http://storify.com/phylogenomics/jgi-user-meeting-day-1-2.js?template=slideshow[<a href=”http://storify.com/phylogenomics/jgi-user-meeting-day-1-2″ target=”_blank”>View the story “JGI User Meeting Day 1-2” on Storify</a>]

I will update the storification tomorrow. If you want to see the full details in a scrolling winder see below

http://storify.com/phylogenomics/jgi-user-meeting-day-1-2.js[<a href=”http://storify.com/phylogenomics/jgi-user-meeting-day-1-2″ target=”_blank”>View the story “JGI User Meeting Day 1-2” on Storify</a>]

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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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OMICS Driven Microbial Ecology …

Quick post here.  Just discovered a nice review paper by Suenaga on targeted metagenomics: Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities – Suenaga – 2011 – Environmental Microbiology

This “Special Issue” on “OMICS Driven Microbial Ecology” has a series of papers, all of which seem to be freely available, of potential interest to readers of this blog including:

and more
Oh, and a paper of mine (with Alex Worden and other members of her lab as well as multiple others)
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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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Evolution rap: 3.5* til infinity #music

Well, after a rough day I am in need of some lightness. And thanks to Eric Lowe, an undergrad. working in my lab, I got a giggle out of 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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Elaine Mardis rocks: nice talk on "Next generation sequencing"

I wish I had seen this before I gave my first lecture on Next Gen Sequencing Methods on Monday.  I will post mine later but here is a really really nice talk by Elaine Mardis from Washington University on the same topic:

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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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Diabetes & H.pylori – a correlation but no known causation despite authors claims

Am having a hard time right now with the comments from the authors of this new paper showing a correlation between H. pylori presence and both type II diabetes and blood glucose levels.  As far as I can tell, the paper does not show any causal connection.  That is, they do not determine if H. pylori infection is a cause of blood sugar issues or a consequence of blood sugar issues.

Yet the authors of the paper, one of whom (Martin Blaser) is a very respected H. pylori expert are saying things like

“This study provides further evidence of late-in-life cost to having H. pylori,”

And they suggest that antibiotic treatment for the elderly may help prevent diabetes.

This to be seems to be a bit over the top.  Yes, it makes sense that H. pylori could cause these issues.  And they have a model for how it might.  But they really should be more careful with their words until a causal connection is established.  After all, we have many well known negative effects of antibiotic overuse, including some shown by Blaser.  The last thing we need is people going out and dosing up on antibiotics in the hope that it will prevent type II diabetes.  But I can guarantee that is what will happen if this story gets overplayed.

At least a few sources report on the lack of anything showing a causal connection (e.g. see US News and World Report):

An expert not involved with the study said that while it did not show a cause-and-effect relationship between the bacterium and diabetes, the findings suggest certain possibilities

But I am worried that that is not enough skepticism to counteract the claims of the authors here. The study is certainly interesting.  And their model for a causal connection is fine.  But they probably need to do a little bit of toning down of their claims here.

UPDATE: 3/17/13

After some people asked me questions about this study at a few recent meetings I dug a little deeper.  And I am a bit startled to find out what the basis is for Chen and Blaser to claim a causative association between H. pylori and type II diabetes/ glucose levels.  Here is a summary of their logic:

Helicobacter pylori is acquired almost exclusively in childhood [8], and there is no clear mechanism for how glucose intolerance present only after the age of 18 would increase risk of H. pylori colonization. It also is unlikely that H. pylori positivity and high levels of HbA1c levels share a mutual antecedent cause because there is no diathesis to both acquire H. pylori and to cause glucose intolerance.

They go on to discuss other lines of indirect evidence for why they think their conclusion is correct.  And some of this is very suggestive.  But “likely” and “suggestive” is not proof.  There are many possible issues with their conclusion.  In particular I think it is easy to come up with a scenario whereby something about the host (either their genetics or their history of exposure or even their micro biome) could influence both whether or not they get colonized by H. pylori or even whether or not they get colonized by particular strains of HP.  And the same factor could influence microbiome interactions later in life.  I see no evidence to indicate that H. pylori is the causative agent here.  And for them to then basically recommend prophylactic antibiotics for elderly with HP seems dangerous at best.

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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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