Friday, March 30, 2012

Nature Precedings - a preprint server for biology akin to arXiv - shutting down as of April 3

Just got this email regarding Nature Precedings.
Dear registrant:

As you are an active user of Nature Precedings, we want to let you know about some upcoming changes to this service. As of April 3rd 2012, we will cease to accept submissions to Nature Precedings.  Submitted documents will be processed as usual and hosted provided they are uploaded by midnight on April 3rd.  Nature Precedings will then be archived, and the archive will be maintained by NPG, while all hosted content will remain freely accessible to all.

Be assured that Nature and the Nature research journals continue to permit the posting of preprints and there is no change to this policy, which is detailed here.

Nature Precedings was launched in 2007 as NPG’s preprint server, primarily for the Life Science community.  Since that date, we have learned a great deal from you about what types of content are valued as preprints, and which segments of the research community most embrace this form of publication.  While a great experiment, technological advances and the needs of the research community have evolved since 2007 to the extent that the Nature Precedings site is unsustainable as it was originally conceived.

Looking forward, NPG remains committed to exploring ways to help researchers, funders, and institutions manage data and best practices in data management, and we plan to introduce new services in this area.  We have truly valued your contributions as authors and users to Nature Precedings and hope that you will actively participate in this research and development with us.
Interestingly, there is no announcement at the Nature Precedings site itself.  I assume the email I received is real (it really looks real) though you never know these days.  It's too bad.  I like the concept of a preprint server for biology.  Interestingly, one of the alternatives to NP is FigShare (which is pretty cool) which recently became part of the Digital Science group which is a sister group to Nature.  Hmm ... wonder what the conversations at joint tea parties between Nature and Digital Science group are like.  Could be fun.

Overselling the microbiome award: Scientists look to mummies for obesity cure

Seriously?  Scientists look to mummies for obesity cure.  I mean - yes - I do think it is possible that antibiotic use has screwed up the human microbiome across the planet and that might have led to other problems.  But for 3$&#$# sake there are 1,000,000 plus other things that have changed since the time of the mummies from diet, to pollution, to longevity, to urbanization, to sedentariness, to TV, to ... well ... almost everything.  So - sure - the microbiome in "the ancients" might be different (I don't see a paper here).  But the headlong "look for mummies for obesity cure" is pretty darn misleading.  And thus I am giving MSN one of my coveted "Overselling the microbiome" awards.

Thursday, March 29, 2012

Why is the paper behind "The Pill Led to Increased Women's Wages" story free to .GOV but not others?

There is an interesting story going around the web.  An example of the coverage is here at the Huffington Post: Birth-Control Pill Helped Boost Women's Wages, New Study Shows.  As for all stories I read about new scientific findings, for this one I looked for the research paper or report behind the story.  The Huff. Post story seemed a bit strange in this regard reporting "Bailey and her colleagues report in a National Bureau of Economic Research working paper due to be published in July in the American Economic Journal: Applied Economics."  Weird - to be published in July.  Why report on it now?  So I sniffed around at other news stories about this topic and found one that said the working paper was published online.  So a little more sniffing (i.e., Googling) led me to the National Bureau of Economic Research (a private non profit entity).  And there, eventually, I found

The Opt-In Revolution? Contraception and the Gender Gap in Wages 

Martha J. Bailey, Brad Hershbein, Amalia R. Miller
NBER Working Paper No. 17922
Issued in March 2012

When I tried to get the paper I discovered it was $5.  Not so bad.  I prefer of course, free and open publication.  Especially if the research and salaries of the authors were paid for by Government grants.  But I did not have the zeal to dig into the funding behind the work.  And 5$ really is not much money.  So I decided WTF - let's buy it. Alas, then I discovered that I could not just buy the paper but that I had to create a user account of some kind, and I stopped at that point.  Too complicated for a bit of a whim.  So much for buying the paper.

Then I saw further down on the page

Information about Free Papers 
You should expect a free download if you are a subscriber, a corporate associate of the NBER, a journalist, an employee of the U.S. federal government with a ".GOV" domain name, or a resident of nearly any developing country or transition economy.

Most of this makes sense to me except the .GOV part.  Why exactly do they make articles available for free to those who work for the US Federal Government but not for others, like, say, the taxpayers who pay for the US Federal Government?  Again, I get that publishers have to make a living somehow and I was even ready to pay for this article because the fee was low and it seemed interesting.  But I am a bit perplexed and annoyed that people that have a .GOV domain address get stuff for free.  This smells funny to me.  You can't even give pencils to some people working for the US Federal Government due to gift rules.  But apparently you can give away research papers that are not available to others.  What is the logic behind this?  Aargh.  Well.  Maybe I will download the paper when I within a .GOV domain.  But it will feel icky in some way.

Quick post: nice review on de novo genome assembly

Just a quick post here.  There is a nice review by Monya Baker on de novo genome assembly in Nature Methods: De novo genome assembly: what every biologist should know : Nature Methods : Nature Publishing Group.  It is currently freely available though not sure if that is permanent or not ...

Love the start which quotes my colleague Ian Korf
Asked how mature the field of genome assembly is, Ian Korf at the University of California, Davis, compares it to a teenager with great capabilities. “It's got bold assertions about what it can do, but at the same time it's making embarrassing mistakes,” he says
The paper is definitely worth a look ...

Wednesday, March 28, 2012

Elsevier: bringing us conference SPAM and also empty privacy policies (literally and figuratively)

Just got an announcement for a meeting from Elsevier that I have absolutely no potential connection too.  It is yet another example of Science Conference Spam.  Not really shocking to get it from Elsevier to be honest.  But one part of the email struck me.  This was the end of the message which I post below:


This email has been sent to xxxxxxx from Elsevier B.V., Radarweg 29, 1043 NX Amsterdam, The Netherlands, using 22 Times B.V. technology and platform. This is a one-off email sent to you in the belief that it will be of interest. We will not add your name and email address to our database unless you request further information. If you wish to ensure that you will not receive a future marketing message from us about these products or services, please send a reply message to We respect your privacy and do not rent or sell your personal information to any non-affiliated third parties without your consent, except as may be stated in our privacy policy at: Elsevier privacy policy.

For the 22 Times privacy policy, please visit: 22 Times B.V. privacy policy.

We obtained your name and email address from ISI Thomson Scientific, 3501 Market street, Philadelphia, PA 19104 USA. If you wish to be removed from the ISI Thomson Scientific mailing lists, please click here ISI Thomson Scientific.
Copyright © 2012 Elsevier B.V. registered office: Radarweg 29, 1043 NX Amsterdam, The Netherlands, under number 33156677, VAT number 002967455B65. All rights reserved.
This is a typical SPAMMY system where you get added to a list without requesting it.  So - want to know what the "22 Times" privacy policy is?  Well if you click the link you get

I can guess what it says but fortunately for those like me that don't read Dutch, Google offers to translate. So I clicked on that offer just to be sure: "Page not found."  Great policy.  Maybe I am supposed to pay to access it?  I note - I have not posted the actual original link in the email because it has what appears to be some tracking information embedded in it.  This I guess is what one could call an empty promise of privacy?

Anyway, next I clicked on the link for the Elsevier Privacy Policy.  This time there is an actual policy there.  Not surprisingly it is not very focused on the people at the other end.  Here it is below, with some highlighting by me

Calling on Nature Publishing Group to return all money received for genome papers and article corrections

Well, let's see if Nature Publishing Group actually does the right thing here.  A few days ago I showed that they were charging for access to "genome sequencing" papers that were supposed to be freely available (see Hey Nature Publishing Group - When are you going to live up to your promises about "free" genome papers? #opengate #aaaaaarrgh).  And in researching this I then discovered that Nature Publishing Group has been charging for access to corrections of articles (see Nature's access absurdity: Human Genome Paper free but access to corrections will costs $64 and Corrections Scamming at Nature: Tantalizing clues, to see errors just pay more money #Seriously?).  

Multiple people from NPG have posted on my blog and twitter that they are working on "fixing" these issues.  By which I think they mean "We will make these freely available again."  But this is not a full fix.  NPG really needs to do a self audit and return ALL money that anyone has paid for access to these articles.  Charging for something that is supposed to be free is not a good thing ... and if they want to really fix the issue they need to give any money they got for these papers back.  Note - I already called for them to do this last year when I wrote about the genome papers not being free.  But I never heard back.  Please help put the pressure on them to do the right thing this time.

Corrections Scamming at Nature: Tantalizing clues, to see errors just pay more money #Seriously?

So - after finding out that "corrections" for freely available papers at Nature cost money to get access to I decided to snoop around at Nature Publishing Group's archives to see how they have handled corrections.

If you search for "Corrections" in Nature Publishing Group's journals, you see that many / most are labelled as "free" and in fact, they do seem to be free.  That is until about 5 years ago.  As far as I can tell, most "Corrections" published prior to September 2007 are not freely available.

For example see this correction where we are told
"In the News & Views article “Chemical biology: Ions illuminated” by Christopher J. Chang (Nature 448, 654–655; 2007) an error crept into part a of the accompanying figure."
Tantalizing.  To find out more you need just pay $18.

Or in this correction:
"In the News & Views article “Organic chemistry:A tuxedo for iodine atoms” by Phil S. Baran and Thomas J.".  
Not so tantalizing.  But nevertheless the full correction can be yours for just $18.

Or this one:
The story ”That's no laser, it's a particle accelerator” (Nature 443, 256; 2006) incorrectly stated that the device described could accelerate electrons to 0.15% of their initial speed.
This is one of my favorites:
"A misleading statement appeared in the News and Views article “Cardiology: Solace for the broken-hearted?” by Christine L."
Want to know what was misleading?  $18.

How about this one:
In Karim Nader's News and Views article “Neuroscience: Re-recording human memories” (Nature 425, 571–572; 2003) the citation of reference 6 was unclear. The reference concerned — Siegel, J.

How about this one
"On page 875 of this Article, there are some typographical errors in the equations used in the computer model. The errors are in the third and fourth full paragraphs on this page." 
Some don't even have any clues.  For example in this one we just know the problem is in an article on Transatlantic robot-assisted telesurgery.  Or in this one the issue is with ancient homes for hard-up hermit crabs.

I could go on and on and on.

The corrections one needs to pay to see go back to the 1800s.  For example in 1893 J. J. Walker wrote:
"The next two paragraphs will require slight modifications accordingly; and the last will, of course, be unnecessary. I owe this correction to a correspondence with which Prof. W.".  Alas, we can't know the rest without - wait for it - without paying $32. 
I think we should have a context.  Find the correction for which the free part is the most absurd or tantalizing.  I don't know if other closed access journals do the same thing but it would be great to know ...

UPDATE: Some more fun stuff from Nature.  There is a paper from Nature in 2005 "Making sure corrections don't vanish online".  It is, of course, available for just $18.

Tuesday, March 27, 2012

Nature's access absurdity: Human Genome Paper free but access to corrections will costs $64

Ahh - the saga continues.  Though I peripherally noted this in a previous post this deserves a post of it's own.  Nature Publishing Group has a policy of making genome sequencing papers freely available.  Alas, not all such papers have in fact been made freely available (see Hey Nature Publishing Group - When are you going to live up to your promises about "free" genome papers?  and A Solution to Nature Publishing Group's Inability to Keep Free Papers Free: Deposit them in Pubmed Central for more on this).

But I have discovered a just painful though funny absurdity with NPG's money making machine.  They have in fact made the Lander et al. Human genome paper from 2001 freely available.  But there is an Erratum to this paper.  And if you want to get it (and without getting it there is no way to know what is being corrected), you have to pay $32: Access : erratum: Initial sequencing and analysis of the human genome : Nature.  Oh, and in addition a Correction "We have identified several items requiring correction or clarification in our paper on the sequencing of the human genome" for this paper also costs $32.  So the incorrect version of the paper is free but the corrections will cost you $64.

I wonder, for papers for which people pay $$, if there are corrections do they get them for free?

A Solution to Nature Publishing Group's Inability to Keep Free Papers Free: Deposit them in Pubmed Central

Well, tick tock tick tock.  I am still awaiting some explanation for Nature Publishing Group once again charging for access to genome papers that they promised would be available for free.  See my last post for more details: The Tree of Life: Hey Nature Publishing Group - When are you going to live up to your promises about "free" genome papers? #opengate #aaaaaarrgh

In the meantime I have come up with a solution even if NPG folks cannot figure one out.  It is very simple.  How about Nature Publishing just deposit's all genome papers in Pubmed Central and thus even when the money making machine of Nature switches some setting and makes the papers not freely available at the Nature web site(s) for some time, the papers will  still be officially free in Pubmed Central.  I think this is probably the only solution I would trust given that this is at least the third time this has happened.

Monday, March 26, 2012

Well, Annapurna has decided laps are for losers; now she curls up on my chest

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.

Saturday, March 24, 2012

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

Friday, March 23, 2012

And now I have a billion plus infinity dollars


Just a typical Friday in #davisca - printing our own money


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.

Thursday, March 22, 2012

OMG - Without a doubt the worst omics word ever - The Sexome

I really have nothing to say here.  I just got pointed to a new paper by Thiago Venancio.  The paper is - I kid you not: Understanding the Sexome: Measuring and Reporting Sex Differences in Gene Systems.  I don't have access to the paper but here is the abstract which is all you need
The current male bias in biomedical research should be eliminated. The large sex differences in incidence and progression of diseases mean that sex-biased factors are an untapped source of factors that protect from disease. Greater understanding will come from intensified study of the "sexome," which is the sum of sex-biased effects on gene networks and cell systems. The global search for sites and mechanisms of sex-specific regulation in diverse tissues will provide unanticipated insights into physiological regulation and targets for novel therapies.
That is without a doubt the worst omics word I have ever seen.  All my previous posts about bad omics words pale in comparison (though I encourage you to read them: Worst New Omics Word Award and bad omics word of the day).

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.

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.

Wednesday, March 21, 2012

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.

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

Tuesday, March 20, 2012

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)

Google Wage or Google Wave? I am interested in Google Wage if they are still offering ...

Just got this email

Google Wage

12:24 AM (4 minutes ago)

Dear Wavers,More than a year ago we announced that Google Wave would no longer be developed as a separate product. Back in November 2011, we shared the specific dates for ending this maintenance period and shutting down Wave. Google Wave is now in read-only mode. This is reminder that the Wave service will be turned off on April 30, 2012. You will be able to continue exporting individual waves using the existing PDF export feature until the Google Wave service is turned off. We encourage you to export any important data before April 30, 2012.

If you would like to continue using Wave, there are a number of open source projects, including Apache Wave. There is also an open source project called Walkaround that includes an experimental feature that lets you import all your Waves from Google. This feature will also work until the Wave service is turned off on April 30, 2012.

For more details, please see our help center.

Yours sincerely,

The Wave Team

© 2012 Google Inc. 1600 Amphitheatre Parkway, Mountain View, CA 94043
You have received this mandatory email service announcement to update you about important changes to your Google Wave account.

Notice anything unusual? How about that it is from "Google Wage?" I assume this is either a really bad typo or a really funny prank from inside Google.

This is both crazy and completely brilliant: The Microbial Academy Of Sciences

Oh My God.  This is so wild and crazy I can't just write OMG - I have to write the whole thing out: The Microbial Academy Of Sciences: What Bacteria Can Discover That We Can't | Co.Exist: World changing ideas and innovation

The article describes an art exhibition in San Francisco in which one part involves giving microbial cultures access to images from space.  The reason for this is possibly captured in this quote
"Because cyanobacteria can perform photosynthesis," Keats says, "they’ll be able to detect patterns of starlight just as human scientists do with their eyes. The difference will not be in their methodology, but rather in the conclusions they reach."
and even better
But in all those eons, bacteria have never been given observatory access, to study the cosmos for themselves. … My observatory is built to address that unfortunate oversight, providing the resources for colonies of bacteria to research a theory of everything, reconciling cosmic and quantum observations in their own bacterial way."
I know some hard core scientists may object to this and some of the other lines by the artist but I personally think this is brilliant (in a devious way but brilliant nevertheless).   Everyone out there should read this article by Morgan Clendaniel.  And I for one and going to try to go to the exhibit ASAP.  I personally cannot believe I have not heard of this yet since it seems to have opened in January ...

Saturday, March 17, 2012

The Axis of Evol: Getting to the Root of DNA Repair with Philogeny

The Axis of Evol: Getting to the Root of DNA Repair with Philogeny 

In 2005 I wrote an essay about my time in graduate school that was potentially going to be included in a special issue of Mutation Research in honor of my PhD advisor Phil Hanawalt.  Alas, publishing my essay ran into complications in regard to the closed access policies of this journal.  So in the end, my essay was not published.  I had forgotten about it mostly until very recently.  And so I decided to convert the essay to a blog post.  The essay is sort of about what I did in grad. school and sort of about Phil ...

Phylogenomics is a field in which genome analysis and evolutionary reconstructions are integrated. This integration is important because genome data is of great value in evolutionary reconstructions, because evolutionary analysis is critical for understanding and interpreting genomic data, and because there are feedback loops between evolutionary and genome analysis such that they need to be done in an integrated manner. In this paper I describe how I developed my particular phylogenomic approach under the guidance of my Ph.D advisor Philip C. Hanawalt. Since I was the first to use the term phylogenomics in a publication, I have decided to rename the field (at least temporarily) Philogenomics.

1. Doctor of Philosophy
When I went to Stanford for graduate school, I was interested in combining evolutionary analysis and molecular biology in a way that would allow me to study molecular mechanisms through an evolutionary perspective. Although I had gone to Stanford ostensibly to work on butterfly population genetics, within two days of starting a rotation in Phil’s lab, I knew that that was where I wanted to work. This decision was somewhat traumatic, since the work on butterflies included spending the summers at 10,000 feet in the Rocky Mountains and possibly chasing butterflies like a Nabakov wanna-be all over the mountain ranges of the world. As an avid outdoor person, this was quite appealing. Nevertheless, I chose to spend 99% of my graduate work in the dingy confines of Herrin Hall, studying DNA repair. The choice of joining Phil’s lab did have one very positive affect – and that was on my relationship with my grandfather on my mother’s side. Benjamin Post was in many ways like a father to me, especially after my father passed away. He was a physicist from the “old school” and thought that most of biology was completely useless. Needless to say, when I told him I was going to graduate school in California (which he considered already one strike against me) to study butterflies, he decided I was simply a lost cause. Despite all his talk of Einstein and computers and math when I was a child, I might as well have been a poet from his point of view. To make matters worse, my grandfather was a crystallographer, and my brother was getting his Ph.D in crystallography at Harvard. When I informed my grandfather that I was going to be working on DNA repair, he seemed somewhat interested. And then I told him, my advisor, Phil Hanawalt, is relatively well known, and actually used to be considered a biophysicist. Then my grandfather really perked up. He said, “Hanawalt – is he related to Don Hanawalt?” It turns out, that my grandfather worked in the same field as Phil’s father (they both did powder diffraction) and knew him. So my grandfather said “You may not be doing real science, but at least you are doing it with the relative of a real scientist.” Thankfully, I was no longer the black sheep in the family. So, with my grandfather’s approval, I embarked on a career in DNA repair.

Friday, March 16, 2012

Want more research funding? Time to give your study organism a better nickname

People who work on pathogens, especially really nasty ones, have built in marketing and fundraising tools. They have nicknames (for the organism, the disease, or both): Good ones. Like "black death" "flesh eating bacteria" "bone break fever" any "wasting disease" any "hemorrhagic fever" "male killer" and more. Now - there are a few non pathogens with good nicknames, like "Conan the bacterium" for Deinococcus radiodurans. But I think we really need to work on better nicknames for non pathogenic microbes. So here are a few proposals:

Any halophilic archaea -> "salt monsters"
Prochlorococcus -> The carbon eater
Rhizobium -> The fixer
Any methanogen -> Fartilicious
Myxococcus xanthus -> The stalker
Nanoarchaeum -> The Hobbit
Tetrahymena thermophila -> The hymenator

Come on everyone.  Let's get some better nicknames.

Thursday, March 15, 2012

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:

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:

Wednesday, March 14, 2012

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.

California Breast Cancer Research Fund Tax Checkoff; wondering about Open Access policies

Just got this email below about what seems to be a worth cause:
March 8, 2012 
Dear UC Colleagues, Throughout California and UC, researchers are developing new approaches to prevent, treat and cure cancer. I am writing you to share important information with those of you who will soon file your California state tax return. At the end of California Tax form 540, there is a section in which you can donate to two highly regarded cancer research programs that are administered by the UC Office of the President.

Tuesday, March 13, 2012

Not sure what to make of this new "Datasets.Com" effort from Hindawi

Just got this email and I thought I would share.  Not sure what to make of this effort.  I do support the sharing of data sets but I am think we probably do not need a whole new cadre of data journals to handle this data.

But there is a spread of what some have called "Predatory" open access publishers (see for example).  Hindawi, who is behind this, seems to have a mix of good and predatory tendencies and this seems like it may fit into the more predatory categorization.  And I just thought it would be good to bring this a bit more into the open to discuss it.

Dear Dr. Eisen,

My name is Safa Tahoon and I am a Journal Developer for the Hindawi Publishing Corporation. We are in the process of launching a new peer-reviewed, open access journal titled Dataset Papers in Genetics, which will publish Dataset Papers in all areas of genetics research, and I am writing to invite you to join the Editorial Board of this new journal.

Sunday, March 11, 2012

Wanted - opinions/details on online systems for annotation of genomes and metagenomes

Doing a little survey/snooping around.  Trying to compile a list of available online tools for annotating microbial genomes and metagenomes.  And I am also trying to get comments on what people think of the various tools.  There are some obvious candidates to think about
But given that there are certainly many many more out there I decided to post a request to Twitter and Google plus and got some responses.

  • Jonathan Eisen ‏ @phylogenomics
    • Researching blog post on free/online microbial genome/metagenome annotation services - looking for examples beyond IMG & RAST
  • Mick Watson @BioMickWatson
  • Ewan Birney ‏ @ewanbirney 
  • Mick Watson ‏ @BioMickWatson 
    • @ewanbirney @phylogenomics @EBImetagenomics needs illumina support, and support of assemblies :/

And from Google Plus where I asked "Researching blog post on free/online microbial genome/metagenome annotation services - looking for examples beyond IMG & RAST ":

Saturday, March 10, 2012

Worst new omics word award: circomics - running circles around my head

Wow - this is really not a good "omics" word.  Check out this paper title and it's abstract Circular DNA genomics (circomics) exemplified for g... [Virology. 2012] - PubMed - NCBI
Circomics was coined to describe the combination of rolling circle amplification (RCA), restriction fragment length polymorphism (RFLP) and pyro-sequencing to investigate the genome structures of small circular DNAs. A batch procedure is described using 61 plant samples from Asia, South America and Central America which revealed 83 contig sequences of geminiviral DNA components and 4 contig sequences of DNA satellites. The usefulness of this approach is validated for the Brazilian begomoviruses, and the sequence fidelity is determined by comparing the results with those of conventional cloning and sequencing of Bolivian begomoviruses reported recently. Therefore, circomics has been proven to be a major step forward to economize costs and labor and to characterize reliably geminiviral genomes in their population structure of the quasi species.
This definitely fits the category of a "bad omics" word which I have history of complaining about but had been ignoring for a bit.  But I am back.  I am giving "Circomics" a "Worst New Omics Word Award" here because, well, it seems completely unnecessary and distracting.

Hat tip to AJ Cann for pointing this one out on Google Plus.

Friday, March 09, 2012

Who is hiring research fellows and/or instructors in microbiology?

A colleague emailed me the following question
 "A good friend of mine is looking for a position as a research fellow or instructor in microbiology with an emphasis on teaching. While she's exploring options herself I figured it couldn't hurt asking; I usually know who is hiring in [my area of expertise] but this is way outside my usual networks, and from what I've been learning positions with an emphasis on teaching are surprisingly rare. Any pointers to departments or groups that might be hiring would be highly appreciated (as are tips on how to find such a position)." 

And alas I did not have a good answer. So, with this person's permission I am reaching out to the blogosphere to see if anyone has suggestions for good places/sources of information about job openings in teaching and/or research fellow positions in microbiology.

Social Biology of Microbes 2012 #SocialMicrobes12 wrapup via Storify

Meeting details: 

Welcoming remarks: 

  • David Relman (presentation) (audio)
  • James Hughes (audio)
  • Lonnie King (audio)

  • Quorum sensing, biofilms, and territoriality (presentation) (audioE. Peter Greenberg, University of Washington
  • Moderator: David Relman DISCUSSION (audio)
SESSION I: Formation and Function of Microbial Communities

  • Moderator: Jacque Fletcher
  • Symbiont community complexity 
    • The fungal gardens of leafcutter ants
      • (presentation) (audio)
      • Cameron R. Currie, University of Wisconsin Madison
    • The role of oxygen in shaping the structure and function of microbial communities
      • (presentation) (audio)
      • Thomas M. Schmidt, Michigan State University
  • Source-sink dynamics: 
    • Marine invertebrate-associated and free-living chemosynthetic symbionts
    • Colleen Cavanaugh, Harvard University DISCUSSION (audio)
SESSION II: Factors Contributing to Community Stability 

  • Moderator: David Relman
    • Social evolutionary theory, cooperation, and the expression of virulence in microbial communities
    • (presentation) (audio)
  • Sam Brown, University of Edinburgh
    • Ecological factors and processes during evolutionary transitions in Darwinian individuality
    • (presentation) (audio)
  • Paul Rainey, New Zealand Institute for Advanced Study & Max Planck Institute for Evolutionary Biology
    • Evolution of cooperation and control of cheating in the social amoeba:
  • Dictyostelium discoideum
    • (presentation: part 1 part 2) (audio)
    • Joan E. Strassmann, Washington University\
  • Swarming bacteria as freight haulage systems (presentation) (audio)
    • Colin J. Ingham, Wageningen University
    • Emergence and robustness of multicellular behavior in bacteria (presentation) (audio)
  • Joao Xavier, Memorial Sloan-Kettering Cancer Center
    • Mathematical and computational challenges in the study of complex adaptive systems
    • (presentation) (audio)
  • Simon A. Levin, Princeton University
    • DISCUSSION (audiopage2image12752 page2image12912 page2image13072 page2image13232 page2image13392 page2image13552 page2image13712 page2image13872 page2image14032 page2image14192 page2image14352 page2image14512 page2image14672 page2image14832

  • Summary of Day One: David Relman (presentation) (audio)
  • Edith Widder, Ocean Research & Conservation Association
    • KEYNOTE: Glowing corpses & radiant excrement: The role of bioluminescence in microbial communities
    • (presentation) (audio)
    • Moderator: Lonnie King DISCUSSION (audio)page3image6024 page3image6184 page3image6344 page3image6504
  • Jo Handelsman, Yale University
    • Interspecies interactions among rhizosphere and soil bacteria (presentation) (audio
    • Moderator: David Rizzo
  • David Low, University of California - Santa Barbara
    • Contact dependent mechanisms of communication in bacteria (presentation) (audio)
  • Vanessa Sperandio, The University of Texas Southwestern Medical Center 
    • Interactions between symbiotic microbes, their mammalian host, and invading pathogens
    • (presentation) (audio)
    • Moderator: Carole Heilman
  • Jonathan Eisen, University of California - Davis
    • Phylogenetic and phylogenomic approaches to studies of microbial communities
    • (presentation) (audio)
SESSION IV: What More Do We Need to Know about Microbial Community Dynamics?
page3image14888 page3image15048 page3image15208 page3image15368 page3image15528 page3image15688

  • DISCUSSION (audio
  • Jared R. Leadbetter, California Institute of Technology
    • Discovery and applications of the metabolic diversity of microbial communities
    • (presentation) (audio)
    • Statistical tools for integrating community networks, spatial and clinical data (presentation) (audio)
  • Jill Banfield, University of California - Berkeley
    • Microbial community assembly and dynamics: From acidophilic biofilms to the premature infant gut
    • (presentation) (audio)
  • David A. Relman, Stanford University
    • Human-microbe mutualism in health and disease (presentation) (audio)
  • DISCUSSION (audio
  • Concluding Remarks (audio

Just got back from a meeting on the "Social Biology of Microbes". Here are some notes from my trip and from the talks at the meeting, done via Storify. Here it is as a slideshow:

And here it is a a full scrollable presentation

Thursday, March 08, 2012

Interesting upcoming conference Exploring Human Host-Microbiome Interactions in Health and Disease

Interesting upcoming conference:

Exploring Human Host-Microbiome Interactions in Health and Disease.

8-10 May 2012 Wellcome Trust Conference Centre
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK

See WT Scientific conferences for more detail.

A day of field guides at #UCDavis and @Wired

Well, how perfect is this.  Today Wired ran a follow up "Birds, Poop and Roadkill: A field guide to Field Guides" to an article that came out last week about my drive for a full field guide to the microbes.  Last weeks article was "Book of Germs: The Quest for a Field Guide to Microbes."  It is by Daniela Hernandez and was a follow up on my talk at AAAS on "A Field Guide to the Microbes" which you can see on YouTube here.  I wrote a blog post with more detail on my obsession with field guides and microbes here.

While Daniela was writing the article I told her about how I collected field guides.  And I sent her a link to a private album I had made of me and my field guides which I am now making public:

For the follow up Daniela and a photographer from Wired Jon Snyder came to my office and lab and took some pictures of me and my field guides (with assistance from Russell Neches in my lab to help set up some of the "scenes).

Here are some pics from their visit.

And now today, the Wired article came out and and amazing coincidence happened.  I was taking a walk around campus with Misha Angrist who is giving a talk at UC Davis today.  And on the walk first we saw a collection of turkeys wandering around campus:

So my birding sense was turned up.  And then we walked across to the UC Davis Arboretum along Putah Creek and bumped into a "birding tour" of the Arboretum.  In six years here I have never seen one of these.  There were some teachers and kids carrying around field guides looking for particular species of birds.

And I note - one even had a field guide I do not have - the "Birds of Northern California" which I will be getting very very soon.  I think today will only serve to boost my obsession with field guides, but that is OK by me.

I note - I love the Wired photo spread of my field guides and my lab.  I particularly am happy that they includes some of the funnier field guides out there like "Flattened Fauna." And I am glad they got in Betsy Dyer's Field Guide to Bacteria because it is one of my favorite field guides of all time.  Thanks to Russell Neches for helping out with it and Daniela Hernandez and Jon Snyder for their work.

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