JOB POSTING: Postdoc with Levente Bodrossy’s lab at CSIRO

We are recruiting a postdoctoral fellow for our new project on high resolution microbial oceanography at CSIRO Marine and Atmospheric Research in Hobart, Tasmania. 

 In particular we are seeking candidates with experience in analysis and/or annotation of genomic and metagenomic sequence data for metabolically-relevant genes using a range of tools (e.g. IMG, Genemark, Glimmer, megan4 etc). The expertise of the successful candidate will be used to: 

– identify candidate functional marker genes for existing and emerging biogeochemical processes through screening of genomes, metagenomes and metatranscriptomes as well as database mining

– assemble and maintain databases of marker genes

– develop high throughput molecular tools based on marker genes, to interrogate the microbial community involved in key processes 

I have attached the job description and would be grateful if you could post this at your institute and/or pass it on to potential candidates.

The detailed job description and application guideline is also available on CSIRO’s website:

To apply, please start here:

Congrats to (Dr.) Migun Shakya!

A well done presentation and defence from Migun Shakya (@microbeatic) today!  Presentation went well and if I wouldn’t have stumped him on the Ammonia oxidizer question would have been a near flawless defence!  Next he is off to the Molecular Evolution course at Woods Hole/MBL for 10 days, finishes up here in Tennessee with final revisions, then a Postdoc at Dartmouth.  Congrats!

Off the charts day for ‘the blog’…

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My little rant last night has apparently caused a bit of fuss. The “Schadtlab” website/blog went from it’s normal 20 or so hits a day (the old record was 90 something), to likely hitting over 500 today.

I’m not sure I would be cut out for real blogging. It’s a little stressful and time consuming. Can’t imagine what it would be like to get 100 times this number if I was doing this for a living, or a celebrity or someone that brought in a ton of hits/comments/etc.

A Rant on Strawberries, Open Access Licenses, and the Reuse of Published Papers

The open access movement in scientific publishing had almost fully converted me.  I have been moving towards publishing more of my work in open access journals for several reasons.  1) The idealist in me likes the fact that anyone, anywhere, anytime can download and read my work free of charge.  Thus likely increasing public/layperson access as well as that of scientists and institutions in the developing world that might not be able to afford access otherwise. 2) The pragmatist in me has noticed than when I add up the open access fee vs. page charges and color figure charges, etc. in traditional journals, they are not all that different. For the most part any small difference there may be will likely be affordable by my research budgets.

Im still ready to make the move towards putting most of my papers in open access journals. I even recently signed up as an editor for the an open access journal (BMC Microbiology).  However in the last couple of weeks at least certain aspects, that primarily have to do with reuse of published papers, have come the fore that bother me.

Anyway, here’s the story.

A few years ago I had the opportunity to host a Ph.D student from Washington State University while she worked in my lab on the analysis of some soil microbial community data derived from organic and conventionally grown strawberry fields.  Long and short of it was we ended up with two pretty good papers out of the work, one describing the overall study in PLoS One (open access from Public Library of Science) and another more focused on the microbial community part in the International Society for Microbial Ecology Journal (from Nature Publishing Group, which features a moving paywall so older articles become free after a year or so).  The PLoS One paper made a bit of a splash, primarily among organic agriculture advocates, because in this case there were clear differences in the cropping systems.  These differences were pretty low hanging fruit so to speak, because the conventional cultivation used the rather extreme practice of fumigating the soil with methyl bromide in an attempt to kill off the all the microbes (good and bad) in the soil.

But thats another story.  If your interested in the details of the science, please download the linked papers (both are now available for free!)

Most open access journals also seem to have an open reuse policy vs. traditional journal where you must get the permission of both the authors and journal publisher to reuse the material (whether it’s just one figure or the whole paper).  I guess I assumed that by paying the open access fee we retained the ability to say yay or nay to reuse (or at least be notified).  Much to my surprise, that is not the case in many open access journals I recently checked out.  Both BMC Microbiology and PLoS one use a version of the same policy from the Creative Commons for example.

This is where the story converges, I promise.

While browsing through my Google Scholar profile page recently I noted this rather strangely formatted entry that features author names where the title should be.  Turns out this  links to a chapter in a recently published book titled Sustainable Soil Management “edited” by Deirdre Rooney and published by Apple Academic Press – CRC Press – Taylor Francis.  Actually I think Apple is the “original” publisher of the book and CRC/Taylor Francis are just distributors, but they are hopelessly inter-tangled so I’m not sure.  Judging by what I can see for free on the Google Books preview, this turns out to be just a lightly reformatted and retitled version of our PLoS One paper.  Not really much editing involved in the traditional sense of the word.

Here is what really irks me about this.  1) Neither I nor the corresponding author had any idea this had been (re)published until after the fact.  Had to run across it on Google like everyone else.  A simple email from the “editor” or “publisher” would have been nice to let us know that they loved our paper so much they wanted to disseminate it in this book.  2) The publishers are charging over $100 for this book.  This, when we already paid when we published this paper to make it freely available!  Not only are we not getting any kickback on this, I was not even sent a complimentary copy as is traditional when you publish in a book! 3) Maybe all the above would be OK if the book just did one thing.  Prominently state (maybe on the 1st page of the chapter and the table of contents) that this is a reprint from the PLoS One paper and cite/link the paper.  This would seem to actually be a requirement of the Creative Commons license linked above (however this is vague and open to various interpretations). Credit in the form of a citation is really the only thing I hope for in anything I publish. As a scientist this is a measure of the importance of the work and that the work is important to others. If the readers of the book don’t know how to cite the original article, it does me little good.  4) Unfortunately I cannot see the whole article on Google Books so I would have to buy the book in order to verify that the PLoS One paper is not credited/cited somewhere.  This is not going to happen. No way. No how. 5) Countless papers are retracted in journals each year where the authors reuse data without citing the original source.  People get fired for this.  I certainly would not want to be accused of this by my institution because an editor or publisher absconded with our paper for some book and didn’t properly acknowledge that it was in fact a reprint.

Anyway, Im not sure who to be more upset with.  The editor and publisher that (re)published the article, or myself for not noticing the reuse clause in the open access license.  From now on I vow that I will pay closer attention to this, and it may influence where I end up submitting future papers.

By the way, if anyone has paid for a copy of this book.  I would appreciate a scanned copy of the chapter…

–Note added 7/3/13–

Please see the comments section below for replies from the publishers and other interesting points of view. It seems there were oversights and errors on a variety of fronts.

Also I received an apology from Dr. Rooney.  Apparently she was misled by the publishers as well, and the publishers have failed to follow through their promise to contact us and give proper attribution. She merely agreed to write a forward to the volume and was not really the editor/selector of the papers included.  I would like to apologize to Dr. Rooney.  I SHOULD HAVE CONTACTED HER FIRST, rather than whipping off this rant/blog entry that partially blamed her.  My apologies.


Announcing PROFESSOR’S Sullivan and Steinweg.

Good news! Two of our postdoctoral associates, Tarah Sullivan and Meg Steinweg, have been offered and accepted Assistant Professor positions starting this fall! Given the tight job market these days I was a little surprised that within one week of each other a couple of months ago, two of my postdocs were in my office to let me know they had received position offers.

Tarah will be moving in October to Washington State University in Pullman to start a position in the Department of Crop and Soil Sciences.

Meg Steinweg will be moving in August to University of Wisconsin – Baraboo to start a position in the Department of Biological Sciences.

As a project manager I’m concerned it is going to leave a big hole in the lab to fill, but as a colleague and mentor I couldn’t be more excited for their success (and even if Tarah is going to my old rival WAZZU)!

Congrats to both!