Author: Emma Ganley

Opening Up Data Access, Not Just Articles


Illustration credit: Ainsley Seago.

For those who’ve been paying attention, you’ll have noticed that we just published an interesting Perspective in PLOS Biology from Dominique Roche and colleagues that provides some practical hints on how to improve public data archiving for scientific research.

And if you’ve been even more on the ball, you’ll also have seen the recent announcement of PLOS’ new Data Policy and subsequent Update on the PLOS website.

The new Data Policy will be implemented for manuscripts submitted on, or after, March 1st. The main change is that all PLOS journals will require that all manuscripts have an accompanying data availability statement for the data used in that piece of research. We’re well aware that this may prove to be a challenge, but we think that this thorny issue needs to be tackled head-on. Ultimately, an Open Access paper for which the underlying data are not available doesn’t make a whole lot of sense.

Roche and colleagues raise some important and interesting points in their perspective and do a fine job of detailing the benefits to the scientific community of making data available. But for the eagle-eyed you’ll note an incongruity between their suggestion that a longer embargo period might be necessary before data need to be made available for some subjects, while the PLOS policy won’t make that distinction.

We don’t all have to agree here, and for the short term this may mean that some choose to send their research somewhere that permits them to keep their data under wraps. But funding agencies are also moving more towards our viewpoint, implementing requirements that data be made available. Whether researchers like it or not, this is something that needs to be addressed; it’s time to start ensuring there are better lab, university and institution practices for the storage and archiving of pertinent data.

If what we really want to see is optimal advancement of science, then open access to research means open access to as much as possible associated with the paper and not just the paper itself.  What should such openness include?  Well – probably everything – from methods to code to materials to equipment.  But without a doubt a key component of openness is access to the data behind a study.  Access to data facilitates reproducibility and testing of a papers conclusions and methods and also enables new discoveries to be made without the expense of redoing the experiments.   We believe that the more open we all are about open data, the more we discuss the benefits and challenges,  and the more we shift the bar towards openness, the better off all of science will be.


Roche DG, Lanfear R, Binning SA, Haff TM, Schwanz LE, et al. (2014). Troubleshooting Public Data Archiving: Suggestions to Increase Participation. PLoS Biology, 12 (1): e1001779. DOI: 10.1371/journal.pbio.1001779


More posts on PLOS Biologue about data:

“Dude, where’s my data?” by Roli Roberts

“Improving data access at PLOS” By John Chodacki

“Dealing with data” by Theo Bloom


Category: Biology, Data, PLOS Biology | Tagged , , , | 18 Comments

Wanted: community ideas about the future of PLOS Biology

About a year ago I wrote a blog post here about becoming the chair of the Advisory Board of PLOS Biology (see From Academic Editor in Chief to Chair of the Advisory Board: figuring out an official role for me (Jonathan Eisen) at PLoS Biology).  One of my main tasks since then involved advising PLOS Biology on the need to improve the diversity of Academic Editors and Advisory Board members.  Just to be clear – I do not work at PLOS Biology – I have a role in chairing the recently created and as of yet not heavily used Advisory Board.  So I figured – I would see how the people who run PLOS Biology would respond to advice.  And at least in this instance (the diversity issue) they responded very well.

So – I guess the next step is to get the Advisory Board as a group to start – well – giving advice.  And to see how PLOS Biology responds to said advice.  Over the next two days I will be talking to some of the Advisory Board members about PLOS Biology and what roles the Advisory Board might play.  Now personally I have a lot of ideas about the directions I would like to see PLOS Biology go in the future.  But I am going to hold off on my personal ideas for now since I would like to solicit input from the community to see what ideas others have about the future of PLOS Biology.

So – here are some questions to hopefully start to stimulate a discussion.

  • What do you think PLOS Biology should focus on over the next five years?
  • What would you like to see PLOS Biology do that it is not doing now?
  • What would you like to see PLOS Biology NOT do that it is doing now?
  • What things is PLOS Biology doing now but should be improved upon?
  • What role do you think PLOS Biology could and should play in the “open access” movement?
  • What other questions should we be asking here?

I am hoping that I / we / you can engage the community in a discussion about the future of PLOS Biology … and would very much like any input here or elsewhere on where you think PLOS Biology should go.


Category: PLOS Biology | Tagged | 24 Comments

Yet another thing for which to blame/thank your mother – your microbes

Wash your hands all the time. Sterilize your kitchen counters. Take antibiotics whenever you have a cough or an itchy throat. Avoid dirt and pets and farms. Do everything you can to keep away those germs.

Such antimicrobial views used to be broadly accepted and beaten into us further by many in the medical community and by diverse marketing efforts.  Sure, we have known about the important role of beneficial microbes in the lives of various plants and animals for many many years. And we certainly knew about some “good microbes” living in and on us. But somehow humans seem to have been generally viewed as – well – bigger than all this.  Better.  Able to go about our daily lives without depending on others.  Especially things so – well – small.

But in recent times, there has been a slow and now accelerating progression towards embracing our microbial connections. Probiotics and prebiotics are everywhere. There are new developments every day it seems on microbiomes (the sum total of the microbes that live in or on an organism) and their role in the human condition.  I go back and forth about how I feel about this.  On the one hand – I am studying microbial communities on plants and animals (including humans) because I believe they play many roles – including many yet to be discovered.  On the other hand, I spend perhaps a bit too much time trying to dampen down the hype in the field.  I blog about “overselling the microbiome” and I try myself to not overstate things.  My biggest fear in giving a talk at TEDMED on the microbes among us which has now been picked up by TED was that I would somehow overstate the importance of the human microbiome.

In the midst of all of this building appreciation about our microbial overlords, there has been one area where humans were somehow still viewed as separate – the womb.  A pervasive view among the medical community and the wider world of scientists and the public has been that we humans are sterile in the womb and that we only get colonized by microbes after birth.  And on top of that there has been the impression that microbial colonization is somehow a mostly random, environmentally based process.

But these notions of colonization semi-randomly after birth are also beginning to change. Now, in a fascinating piece in PLOS Biology Funkhouser and Bordenstein discuss how in the animal world maternal transmission of microbes to offspring is pretty much the rule. And they also discuss how this seems to be the case in humans too.  We are in fact not (apparently) sterile in the womb.  And vaginal birth and breastfeeding can be viewed largely as delivery mechanisms for microbes (and the food for the microbes).

Check out their Figure 1 for a summary of some of the details they have collated about maternal transmission of microbes in humans.

“Sources of microbial transmission in humans from mother to child.” from Funkhouser LJ, Bordenstein SR (2013) Mom Knows Best: The Universality of Maternal Microbial Transmission. PLoS Biol 11(8): e1001631. doi:10.1371/journal.pbio.1001631

Of course, in retrospect this all makes sense. Many key properties of animals actually come from symbioses with microbes. And for the mutually beneficial interactions it would make further “adaptationistic” sense that mothers would want to deliver good microbes to their offspring. Now of course, just because someone can make up a just-so story about how such a transmission should be beneficial does not mean that (a) it is beneficial or (b) such a transmission would evolve. But as they document in their paper maternal transmission of microbes (good and bad mind you) is a pervasive feature of animal life.  So why should such things not happen in humans?

In fact, I would argue that the argument of Funkhouser and Bordenstein does not go far enough.  Why limit the concept to animals.  Certainly, as we learn more and more about the importance of microbial communities in the life of plants, we might expect to find similar delivery and feeding mechanisms to be pervasive in the plant world too.  And of course, there are other multicellular organisms out there beyond plants and animals that also depend on microbes for many functions.  Consider many fungi – which have extensive microbial interactions.  And kelp (a brown algae – not closely related to plants) for which the microbial interactions are now being examined in more and more detail (e.g., see Michelou et al. 2013).  And of course many microbes themselves likely have evolved detailed mechanisms for transmitting symbiotic (other) microbes to their offspring.

So what does this all mean?  Of course, just because microbes are delivered to offspring does not mean that those microbes are “good” for us – as “bad” and “neutral” microbes can also be delivered too.  However, this perspective certainly means that for studies of humans we really need to delve much deeper into the ways that microbes are transmitted from parent to offspring and how activities like breastfeeding affect the establishment of microbial communities.  And, it does give everyone a convenient excuse if something goes wrong with their microbial community.  You can just blame mom.  But if things go well, perhaps everyone should remember to thank their mother.  After all, “Mom Knows Best.”

Full citation of the referenced paper:

Funkhouser LJ, Bordenstein SR (2013) Mom Knows Best: The Universality of Maternal Microbial Transmission. PLoS Biol 11(8): e1001631. doi:10.1371/journal.pbio.1001631

Thanks to Keith Bell for (though a bit aggressively) making me continually reconsider the notion that humans are sterile in the womb.


UPDATE 8/22 12:52 PM PST:

Check out the blog post by author Seth Bordenstein about the paper: The Story Behind “Mom Knows Best: The Universality of Maternal Microbial Transmission”

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Working to increase diversity of PLOS Biology Academic Editors and Advisory Board members

In the last few years I have spent a lot of time thinking about, and worrying about, the diversity of people involved in various aspects of the life sciences.  One area I have focused on extensively has been presenters at conferences (see some of my posts on this topic on my Tree of Life blog here).  In one recent online discussion about a conference I felt was heavily biased towards male speakers, a responder said something to the effect of “Oh yeah, well, what about the diversity of Editorial Board and Advisory Board members at PLOS Biology?”  And, well, they were right.  We do in fact have a less than ideal sampling of diversity there.  Two aspects of diversity in particular are, I think, in need of work – representation of women, and international coverage.  So as the new Chair of the PLOS Biology Advisory Board, I have decided that working on this diversity issue will be my main first task.

Fortunately for me, the PLOS Biology team has been not only very receptive to tackling the diversity issue, but has already been developing a plan to tackle it for some time.   Our goal for now is relatively simple – increase representation of women and people not from the US on the PLOS Biology Editorial Board and Advisory Board activities.  A key question however is – how do we achieve this goal?  To answer this it is necessary to figure out where the bottlenecks are in representing diversity in these groups.

Clearly, one possible bottleneck lies in invitations to join the Editorial Board and Advisory Board.  The path to becoming a member of the PLOS Biology Editorial Board is relatively simple – the PLOS Biology Editorial team invite new people to serve as Guest Academic Editors (so called Guest AEs) for a few papers.  If they do “well” then they can then be invited to be official Editorial Board Members.  So – we plan to do targeted Editorial Board recruitments to increase the diversity of people invited to be Guest AEs.   For the Advisory Board, the approach is somewhat similar – the PLOS Biology Editors identify what one could call “Super” AEs (labelled as such due to their workload and general commitment to the journal, often going beyond the normal call of duty of Editorial Board members), and these people are invited to join the Advisory Board.  We also plan to do targeted recruitments to increase the diversity of those invited to be on the Advisory Board.

But of course, just inviting people is not enough.  One needs to get people to (1) hear or see the invitations; (2) to consider the invitations seriously; and (3) to accept them.  In my experience in dealing with diversity issues at conferences, it seems that #1 and #2 are actually quite challenging.  People are overwhelmed with email and meetings and schedules and responsibilities.  So if you just send out a bunch of email invitations to a few extra people, if you only hear back from a small % of people you invite, this may not be too useful.  Same with the Editorial Board I suppose.  An email that says

Dear Dr. So and So.  We are inviting you to take on a new responsibility that involves extra work for you.  In exchange we can offer you no payment and little recognition

is probably not going to excite some of the key people you want to get involved.  So some more personal contact is almost certainly going to help.  This of course takes time, and some effort.  But it is probably worth it.  Fortunately, PLOS Biology is relatively unique in the biology journal world in that the Editorial Board members do little if any of the “grunt work” and can focus on the science.  The PLOS Biology Editors handle the main tasks of screening submissions, recruiting Editorial Board members to serve as Academic Editors, and making recommendations for reviewers.  The job of the Academic Editors is to advise the staff on whether a paper should be reviewed, and who good reviewers might be.  But the invitations to review and the chasing down of reviewers is done by the  journal staff.  Then, when reviews come back in the PLOS Biology Editorial team read through them, summarize them, and make a recommendation for what to do next.  They then consult with the Academic Editors to get their input on the reviews and the recommended course of action.  It is actually a relatively pleasant experience for AEs, to tell you the truth.  If more people knew how this worked, I have a feeling that more would say yes to invitations to be on the Editorial Board (some more detail on the process is available here: From Academic Editor in Chief to Chair of the Advisory Board: figuring out an official role for me (Jonathan Eisen) at PLoS Biology).

Plus of course another way to get people to say yes is to tell them that there are free to say no for specific requests whenever they are too busy.  What you want is for people to want to help you, not to feel they have to help you.  In the end, my goal as the Chair of the Advisory Board is to have PLOS Biology serve as a model for strong representation of diversity on its various Boards.  This may take some work, but it is important work.

And while I am at it, I think I would like to crowdsource this activity by asking for others to help.  Do you know strong open science advocates who are also good scientists who might be interested in getting more involved?  Are you perhaps such a person?  Send me / us the names and any other information by email or post comments here.

Finally, I want to add, that I realize that simply increasing the number of women and international representatives on the various PLOS Biology Boards is not the only aspect of diversity that we can or should tackle at PLOS Biology.  But it is a start.  And part of the start is to be more open about discussions of these issues.  In that regard, if any readers have experience with ways to increase diversity in STEM (science, technology, engineering, and mathematics) fields, or for that matter, other areas of academics,  it would be great to hear about it in comments.

Category: PLOS Biology | Tagged , , , , , | 22 Comments

From Academic Editor in Chief to Chair of the Advisory Board: figuring out an official role for me (Jonathan Eisen) at PLoS Biology

Well, three+ years ago now I accepted a role as “Academic Editor in Chief” of PLoS Biology.  I wrote an Editorial about why I was interested in Open Access publishing (see PLoS 2.0) and was excited to be helping out with PLoS in a more formal role.  However, exactly what that role was going to be was unclear.  You see, PLoS Biology is what one could call a “hybrid” journal.  It has full time editors who run the day to day operations of the journal, kind of like what one sees at Nature or Science and some other similar journals.  Generally, we (me and various friends) refer to these full time editors as “Professional Editors.”  This is because PLoS Biology also has editors who are active researchers or educators or both who serve to advise the Professional Editors on decisions about submitted articles.  These editors are referred to as “Academic Editors.”  Thus the concept of a “hybrid” journal with both Professional Editors and Academic Editors working side by side, hand in hand.

When I was recruited to become the “Academic Editor in Chief” I became in a way, the head of the advisors on decisions.  In other words, I was not in charge of anything.  The Professional Editors made the final calls on pretty much everything – day to day operations, front matter, policies, manuscript decisions, etc.  And I was generally fine with this.  After all, I am an Academic.  I am busy.  And there were full time professionals to run the journal.  The #1 complication in this whole arrangement has been that people from the outside have no idea what “Academic Editor in Chief” means.  Sometimes that is good for me (they think I do more than I do).  And sometimes it is bad (when people want to complain about something done by PLoS Biology they frequently write to me, especially if they know me).

I thought it would be useful for everyone out there to give a general outline for how manuscripts are reviewed at PLoS Biology.  Manuscripts and pre-submission inquiries go to the Professional editors.  They “triage” these submissions and reject those that fall outside of the PLoS Biology scope or do not meet some aspect of the PLoS Biology publishing criteria.  For those that make it through this screening, an Academic Editor (AE) is then consulted to work with the professional editors on deciding whether or not the manuscript is suitable to send out for review.  If the decision is “yes” then the AE also works with the staff to come up with a list of potential reviewers.  Once reviews come back, they are sent to the AE and then this person works with the professional editors to make a decision about whether the paper is then accepted, accepted pending revisions, or rejected.  In my experience, most of the time the professional editors go through the reviews and make a recommendation as to what the decision should be and then ask the AE if they agree or disagree.  If the AE disagrees, there is a back and forth about what to do and then a decision is made.  In my experience as an AE, the decisions have always been agreed upon in the end (well, by the Editors, not necessarily by the authors).  But in the grand scheme of things, the Professional Editors are the final decision makers.

So as PLoS Biology is starting a new blog I thought – this would be a great time to explain to everyone what my role is and isn’t.  Well, it is easy to say what my role isn’t.  I am not responsible for decisions on manuscripts unless I am the actual Academic Editor consulted for a paper – and then I would have the same role as any AE (as outlined above).   In other words – though people may want to give me credit or blame for ALL the decisions at PLoS Biology, really, that credit and blame should go to Theo Bloom – the “Chief Editor” (a.k.a. the head of the Professional Editors).

Alas, it is much harder to say what my role has been.  Theo and others at PLoS consult me about various issues and I make suggestions to them (sometimes on solicited topics, much of the time on unsolicited topics of my choosing …).  But I haven’t had actually ANY formal responsibilities.  That is, until now.  In conversations with Mark Patterson (who was head of publishing at PLoS) and Theo Bloom and many others at PLoS Biology we have actually come up with something for me to do.  I am going to become the head of the PLoS Biology Advisory Board.  This Board will be made up of a collection of Academic Editors who have been most deeply involved in the journal.  What will the Advisory Board do?  Well, see Theo Bloom’s answer below …


So what will the Advisory Board do? Theo Bloom explains...

Jonathan outlines the process well. Why do we do things this way? As a team with decades of combined experience in several different journal models, the team who launched PLoS Biology in 2003 felt, and I agree , that professional editors bring certain strengths to the job and academics bring others. For example, professional editors can drive greater speed of decision making; it is, after all, our only and full-time job, and we share office space with the excellent administrative team for the journal. We also show no fear or favour: our next job (or grant) is not dependent on pleasing one author or another. And we can ensure consistency across fields by working together as a small team. But we readily admit that this small team cannot possibly provide the depth of insight in multiple fields that academic editors can: they know their field, its frontiers and its people (including rising young stars) much better than we can. So, we feel that a partnership brings huge benefits to the authors we’re here to serve. We have over 100 academics in different fields on our editorial board and yet we still often get papers that none of them feels comfortable handling – but we’re never more than one referral away from someone who knows the field well. And some members of our board are called on much more than others. We cannot dictate who submits what to the journal, so some board members are called on only a handful of times per year while others hear from us every month.

So, our decision to build an advisory board reflects at least two major aspects of the way we work with academic editors: that some editorial board members work with us frequently, and that some of them also weigh in more substantially on editorial issues and matters of journal policy and practice, not just on individual papers in their field.  Appointing such committed academic editors to the advisory board is also our way of acknowledging the time and work they invest in PLoS Biology. Our advisory board members, chaired by Jonathan, will be our first port of call as we continue numerous discussions about peer review, plagiarism, data handling, publication ethics and how we develop PLoS Biology. In Jonathan’s formal role as chair of this group, and informal one as evangelist for PLoS and PLoS Biology, he will have a more manageably sized group to consult first with new ideas.

The editorial team of PLoS Biology look forward to working with Jonathan and the new Advisory Board over the coming months.

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