Thursday, April 09, 2015

Today's Spammy journal Editorial Board Offer #1

Just got this - pretty lame given that, well, I do not do anything related to this journal.

Dear Dr.Jonathan A Eisen,   
Hope this mail brings you good health and prosperity 
Fisheries and Aquaculture Journal is successfully publishing quality open access journals with the support from scientists like you. We are aware of your reputation for quality of research and trustworthiness in the field of science and thereby we request you to be an Editorial Board Member of our Fisheries and Aqua culture Journal. It would be our immense pleasure to have you as one of our editorial board member. 
Please follow the below link for more information you are interested, you are requested to send 

  • A recent passport size photo (to display at our website) 
  • C.V
  • Biography
  • Research Interests for our records 
Kindly submit your details at We look forward to a close and long lasting scientific relationship for the benefit of scientific community.Waiting for a positive response.
With Kind Regards,XXXEditorial Assistant 
Fisheries and aqua culture Journal7 
31 Gull Ave, 
Foster City CA 94404, USA

Wednesday, April 08, 2015

More microbe-themed art - the Eden Project's "Human Biome"

Just got pointed to this Wired article by Katie Collins -- Eden Project's 'Human Biome' is a gross, musical microbe showcase (Wired UK)

Fascinating project that I actually don't think is gross in any way.  From the article

Invisible You: The Human Biome will explore the community of microbes that live in and on each and every one of us. Artistic and interactive displays will show bacteria, fungi and viruses, with 11 artists commissioned to create works for the exhibition.
I want to just quote the entire story but I think that is not allowed so let's just say you really should read the whole thing and look at the gallery.

Sunday, April 05, 2015

Glyphosate, Roundup, GMOs and the microbiome part 1: crowdsourcing literature

For many reasons I have been interested for the last few years in how agricultural practices affect microbiomes.  For example in regard to crops, how do farming practices affect the microbiomes of the plants, the microbiomes of the soil and area around the plants, and the microbiomes of organisms (including humans) who make use of the plants?

I won't go into all the detail right now for why I am interested in this topic but for some examples of my work in this area see The microbes we eat abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types and Structure, variation, and assembly of the root-associated microbiomes of rice.

Anyway, the reason I am writing this now is that tomorrow I am "testifying" to a NRC Committee about this topic and some related topics.  The presentation will be shown live online (register here).  And I thought, in the interest of openness, I would post some of what I am thinking about here before hand.

One of the key topics for tomorrow is something I have been snooping around at for a few years - how does glyphosate (the key ingredient of RoundUp and a widely used herbicide) affect microbiomes?  I am interested in this from both a scientific point of view (I think it is an interesting topic) and also from a "public policy / education" point of view.  I think this is a really good topic to have a public discussion of "microbiomes" and both the importance of microbial communities and the challenges with studying them.  So a few years ago I started thinking about working on this and developing a "Citizen Science" project around it.  And, well, I am still working on that idea and probably will be trying to launch something in the near future.  As a first start I thought it would be good to start to engage the community (researchers, teachers, the public, etc) in a discussion of this topic.  So .. this is the beginning of that I guess.

Some questions I think are interesting:

  • Does glyphosate affect plant microbiomes?
  • Does glyphosate affect soil microbiomes?
  • Does consumption of plants treated with glyphosate affect the microbiomes of the consumer? 
    • Directly (e.g., by glyphosate itself being in the food and directly affecting microbomes"
    • Indirectly (by glyphosate affecting the microbiome of the food which in turn affects the microbiome of the consumer)
  • If glyphosate affects any of these microbiomes above, are these significant affects (e.g., in terms of health)?
Now I am not the only person who is interested in this topic.  In fact, there have been many people looking into these and related topics for years.  Some of the things I have seen on this topic in the popular press and the scientific literature are, well, not good science.  And some of the things I have seen are fascinating and well done. 

So as a first step in looking into this, I scoured the literature for papers of interest.  And that is really why I am writing this.  I created an open collection of the papers I have found with the Zotero reference collection system.  See this link for the collection.  And if you know of any other papers truly related to this topic, please add them to the collection (learn more about Zotero here).  I do not profess to know everything about this topic.  But I think it is interesting and possibly important.  

Wednesday, April 01, 2015

Four simple tools to promote gender balance at conferences - guest post from Julie Pfeiffer @jkpfeiff

Guest post from Julie Pfeiffer.

Julie Pfeiffer
Associate Professor of Microbiology
University of Texas Southwestern Medical Center

Four simple tools to promote gender balance at conferences 

1. Know that you are biased. Identify your biases.

We all have biases and many of them are unconscious. You can discover your own biases using online social attitude tests developed by Project Implicit, a non-profit organization affiliated with Harvard University. The Gender-Science Implicit Association Test is particularly relevant here. It turns out that I have moderate bias linking science with males, as well as other biases. Knowing this fact has been extremely important. It is very difficult to alter unconscious bias, but it is easy to understand that you are biased and edit your actions accordingly. For example, if I need to make a list of potential speakers or authors quickly, the list will be of senior men from the United States. The key is to spend time EDITING the list to ensure diversity.

2. Keep track of numbers.

Most individuals in leadership positions are not seeking to exclude women or other groups from plenary talks, career opportunities, etc. Instead, they simply forget to count. They forget to keep track of gender ratio and other types of diversity. They forget to edit. When leaders/organizers have diversity in mind, diversity is relatively easy to achieve. Two examples illustrate this point:

1) Vincent Racaniello is President of the American Society for Virology and his goal was to put together an outstanding and diverse group of plenary speakers for the annual meeting in 2015. He asked for speaker suggestions via emails and Twitter ( He made a list and he edited it. The result? The best representation of female scientists at a conference I have ever seen--- 50% of the plenary speakers at ASV this year are female.

Monday, March 30, 2015

Painful, kind of hilarious, typesetting error in a #PLOSOne paper from my lab - should I try to get it fixed?

Saw this tweet:

So I went and found the paper.

Wu D, Jospin G, Eisen JA (2013) Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups. PLoS ONE 8(10): e77033. doi:10.1371/journal.pone.0077033

And discovered what he was pointing to

Then I looked at the Pubmed Central version of the paper and it was the same.  So I wnet and found the arXiv version of the paper and it looked correct.

Sunday, March 29, 2015

Calling attention to meetings with skewed speaker gender ratios, even when it hurts, part 2

A few weeks ago I gave a talk at the Future of Genomic Medicine 2015 (aka #FOGM15) meeting.  The talk seemed to go over well.  I talked right after Martin Blaser in a session on "The Microbiome".  I posted my slides and then a video of my talk as well as notes from the meeting: see My microbiome talk at #FOGM15 - the perils (and fun I guess) of redoing one's talk at the last minute.  And I met some really interesting people at the meeting and enjoyed most of the talks I went to.

But alas, one thing stuck in my head from this meeting.  One single Tweet from someone out there threw me for a loop:

And this let to a bit of soul searching on my part.  Some of the conversations on Twitter are captured in this Storify:

Which I guess culminated in a post to the organizers of the meeting

Saturday, March 28, 2015

How to keep up with microbial ecology and the built environment: microBEnet is your place

Just posting a wrap up of posts on microBEnet (where I blog frequently as do many other folks that work on something related to microbial ecology, the built environment, or the intersection of the two).  microBEnet is really becoming a central place to find out what is going on in the world of microbial ecology and the built environment.  And I love that we are getting more and more posts from outsiders about their work, their meetings, their ideas and more.  Anyway - here is a wrap up of the posts for the last month.  If you are interesting in joining microBEnet and writing posts about relevant topics, let me know.

Jenna Lang (staff scientist in my lab) -- meeting reports from a Planetary Protection meeting
My posts:
Alexander Sczyrba on the Critical Assessment of Metagenome Interpretation (CAMI)

Wednesday, March 25, 2015

Calling attention to poor speaker gender ratio - even when it hurts

So I saw this Tweet earlier today

And that sounded very interesting. So I clicked on the link to check out the Plant Breeding for Food Security: The Global Impact of Plant Genetics in Rice Production A symposium honoring Dr. Gurdev Khush symposium.  And, then I went to the program.  And sadly I saw something there that was not to my liking.  The speakers were almost all male (men labelled in yellow, women in green)
  • Welcome to the Khush Symposium (Alan Bennett)
  • The Plant Breeding Center (Charles Brummer)
  • The Confucius Institute (Glenn Young)
  • Global food production – challenges and opportunities (Ken Cassman) Food production, technology and climate (David Lobell)
  • Panel – Impact of Gurdev Khush on plant genetics and food security Tomato genetics
    • (Dani Zamir)
    • (Pam Ronald)
    •  (Gary Toenniessen)
    •  (Gurdev Khush)
  • Lunch; The California Rice Industry (Kent McKenzie)
  • The rice theory of culture (Thomas Talhelm)
  • Recent advances in rice productivity and the future (David MacKill)
  • Hybrid rice technology contributions to global food security (Sant Virmani)
  • Super green rice (Qifa Zhang)
  • Tackling the wheat yield barrier (Matthew Reynolds)
  • African Orphan Crops – inspiration and execution (Howard Shapiro/Allen Van Deynze)
If this was a symposium outside UC Davis the first thing I would do would be to post about it.  To Twitter or my blog or both.  And to critique them.  Why?  Because there is a bad history in STEM fields of having meetings and conferences have under-representation of women as speakers.  And this has become a passion of mine and I write about it a lot.  But I hesitated.  Why?  Because this was from UC Davis and many of the people involved are friends / colleagues.  I did not want to anger them, or embarrass them.  And I don't think there is any intentional bias here by any means.  But, if I am going to critique people outside UC Davis, it seems like I should also apply the same standards to people inside UC Davis and to colleagues and friends.

So I posted to Twitter a response:

But that did not seem sufficient.  So I wrote up this post.  Underrepresentation of women as speakers is a serious issue in STEM fields.  And it is solvable (e.g., see Some suggestions for having diverse speakers at meetings by myself and the wonderful Ten Simple Rules to Achieve Conference Speaker Gender Balance by Jennifer Martin).

Now - do I know who the possible speakers were for this symposium?  No - I don't really know the field.  Is it possible that there just are no women in the field?  Sure.  But I would bet anything that is not the case here.  Having a meeting where the ratio of speakers is 16:1 male: female sets a bad example.  UC Davis and the organizers of this meeting can do better.  And though this will possibly hurt me in various ways (I already got grief from one person who I will not name for the Tweet), I think it is critical that we call out examples such as this.

And finally I note - I have taken on the issue of women at STEM conferences and meetings because, well, it is easy to identify cases where the numbers are anomalous and it is relatively easy to solve.  But it is also important that we consider other aspects of diversity of speakers (age, ethnicity, career stage, etc).  It is important to have diversity of speakers at meetings for many many reasons.  Speaking is a career building opportunity.  Speakers serve as role models for others.  Diverse points of view are important to have represented.  Bias - whether simplicity or explicit damages the whole practice of science.  And more.  Yes, we need to work on many aspects of diversity in STEM fields.  Improving the diversity of speakers at meetings is but one part of this.  But it is an important part and it is relatively easy to do.  So just do it.  And call attention to it.  Even if it hurts.

Treponema are not "ancient" but absence from some human's guts is very interesting

So I saw some Tweets today that caught my attention, discussion news stories about "ancient" bacteria being missing from some human's gut microbiomes:

These refer to a sadly inappropriate headline in Science

What is wrong with this?  Well, there are no "ancient" bacteria around today.  They are all modern.  I am not even sure what they were trying to say.  Just a really bad evolution argument I guess.  I pondered giving Science a Twisted Tree of Life Award which I give out for exactly this kind of thing -  but decided first to dig into the science here and gloss over the bad evolution headline.

And it turns out - what the news story is about is in fact interesting - a new paper out in Nature Communications:  Subsistence strategies in traditional societies distinguish gut microbiomes.

The paper is freely available and has some really interesting material in it.  They key to me - at least related to this "ancient" bacteria claim is the following part of their abstract:
As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2–2.5 MB, coverage depth × 26–513) and functional potential characterization, we discover these Treponema are diverse, fall outside of pathogenic clades and are similar to Treponema succinifaciens, a known carbohydrate metabolizer in swine. Gut Treponema are found in non-human primates and all traditional peoples studied to date, suggesting they are symbionts lost in urban-industrialized societies.
And then some further detail in the paper:
Although Spirochaetes have been previously reported from the gut microbiome of non-human primates and ancient human populations, they have only been observed in high abundance among extant human populations with non-Western lifestyles, such as a traditional community in Burkina Faso and a hunter-gatherer community in Tanzania. As such, they may represent a part of the human ancestral gut microbiome that has been lost through the adoption of industrial agriculture and/or other lifestyle changes. 
So they don't go into the full detail here but what I think they are saying is that they infer that human ancestors had Spirochaetes (based on the finding of it in non human primates and some human populations).  And thus they further infer that human populations (e.g., the people they studied in Oklahoma) that do not have these Spirochaetes have "lost" them.

I note - I think this terminology of "loss" they are using is not quite right here in a way.  Saying that these Spirochaetes have been lost implies to me that they are heritable.  But they do not in fact show that.  It could be that these are related to diet or environment in some way - something shared by some human populations and non human primates, for example.  And thus the absence from some "Westernized" populations could be more of an environmental thing than a "loss" in the past.