Overselling the microbiome award: Dr. Raphael Kellman at MindBodyGreen

Well this article by Dr. Raphael Kellman has just lots of overstatements about the microbiome: Why The Microbiome Is Your Key To Glowing Skin & Healthy Weight

For example, he writes:

Have you and your boyfriend or girlfriend ever gone out for a feast of delightfully unhealthy proportions only to then find yourselves picking fights with one another once you're back home and digesting?  Fueling your body with unhealthy bacteria, and then feeding it with more unhealthy bacteria, is a sure-fire way to destabilize your mind-body connection. Instead, focus on supporting the positive bacteria in your belly with fermented foods like yogurt, sauerkraut, and kefir and watch your spirits soar.

This implies that somehow the microbome has some role in such situations and in mediating the relationships between two people.  And it implies that that can be fixed with fermneted foods.  And this is without any shred of evidence ...

Then there is a discussion that makes the microbome sound like the master controller of all that is human:

Our bodies are cohesive entities, yes, but within each there are several languages spoken. 

The microbiome works like a translator for all of these systems, deciphering and decoding so that one process can communicate with the other for more efficiency and effectiveness (helping our systems to work as a team instead of independently alongside one another).

And then there is evidence free claims about fatigue and the microbiome

I've found that this kind of unexplained fatigue is often linked to a lack of diversity in the microbiome and can be remedied, despite what conventional medicine says

Whenever someone critiques "conventional" medicine and then presents no evidence for their claims, one should be wary, very wary.

And it ends with

Your inner ecology, your microbiome, is influential on your physical health, and that shows through glowing skin, a balanced weight and a youthful essence.  

So - if you want to be youthful and glowing and have good sex and relationships and get rid of your fatigue and fix your automimmune disorders and obesity and connect all of your systems together, all you have to do is fix your microbiome.  Simple.  Oh and how do you do that?  Why funny you asked, because I am selling this new book on the Microbiome Diet to solve all your problems.  Ridiculous.  And dangerous.

And thus I am giving out an Overselling the Microbome award to Dr. Kellman.

Some silly microbome ideas from @DeepakChopra and @rudytanzi

Well, just got to reading this: Big Idea 2015: Medicine, Wellbeing, and the Microbiome | Deepak Chopra MD. Yes, it was from December 2014 but I could not get up to reading it then because I saw some of the comments online about it and it seemed off.  But anyway I caught up to it today.  It has many inaccurate and misleading statements about microbes and microbiomes I just felt like I had to post something.  Some of the problemmatic parts are below with comments.

Let's start gently.  As with many other stories on the microbiome, this article quotes the oft cited "fact" of a 10:1 ratio of microbial cells to human cells.

By some estimates the body has between 35 and 100 trillion cells with only 1 in 10 belonging to tissues and organs and the rest belonging to the microbiome.

This has been refusted by a great article in the Boston Globe by Peter Andrey Smith in September 2014 (long before this was published): Is your body mostly microbes? Actually, we have no idea.  Yes, I and many others cited this 10:1 ratio before the Globe.  But seeing it cited in this from December 2014 suggests Chopra and Tanzi aren't really paying attention to microbiome science.

The next comment I find a bit off is the follwing:

Our personal human genome also determines the composition of our microbiome, which in turn can influence metabolism and propensity for weight gain.

Sure.  Our genes influence out microbiome.  But "determines the composition" is way to strong a statement.

But the things that got to me most were many of the comments supposedly about evolution.  I list some of them below:

• This varying ecosystem isn't populated by foreign invaders and pathogens but by colonies closely connected to human evolution.
• I don't even know what this is supposed to mean.  These are not "colonies" first of all.  And second, what does "connected to human evolution" even mean?  And wouldn't pathogens be connected to human evolution?
• The microbiome interfaces between the human body and the outside world in complex ways, but the gist is that human DNA has evolved in cooperation with microbial DNA. This fact is more important than the interactions that cause diseases created by invading bacteria and viruses.
• Re "human DNA has evolved in cooperation with microbial DNA".  Well, sure.  Some of the microbes we live with are mutualists. But most likely only a limited number of mutualistic interactions are going on.  This sounds like a Gaia type of model, with no evidence.  
• And then "This fact is more important than the interactions that cause diseases created by invading bacteria and viruses."  Really?  More important than the plague?  Than malaria? Aids?  Cholera.  TB? Worms? And more.  This sounds really silly.
• Mitochondria actually have their own genomes inherited from the mother without change.
• Umm - no mitochondria mutate and change, well, all the time.
• Some of the most archaic microorganisms on Earth survive today in our microbiome.
• This is without any justification.  First of all - what does "most archaic" mean?  And second, if it means what I think it means (organisms that have features like those from billions of years ago) - well - no - the human microbiome does not have a lot of such organisms.  This is just complete hooey.  
• It would appear that the genome and the microbiome cross-talk, a conversation that has been continuing for billions of years with no signs of stopping.
• What does this even mean?  In what way has the human microbiome been interacting with the human genome for billions of years.  In what way have human ancestors been interacting with microbiomes for billions of years?

Yes, the microbiome is important.  But this "essay" is filled with nebulous pseudoscientific comments about the microbiome all, apparently, to sell an upcoming book and related activities

"In an upcoming book we are co-authoring, Super Genes, we will present the latest findings as well as a lifestyle program devoted to what we call Self-Directed Biological Transformation"

Right now, I don't think Chopra and Tanzi show any evidence they really understand the microbiome .. doesn't bode well for their book and lifestyle program.

Horizontal gene transfer into humans? I am not convinced. Full text of my comments to reporters here

Some news stories about a new paper claiming evidence for horizontal gene transfer into humans and other chordates. I got asked by many reporters about it and some used some of my email comments in their articles.

See for example

• Horizontal Gene Transfer a Hallmark of Animal Genomes? in The Scientist by Jyoti Madhusoodanan
• Humans may harbor more than 100 genes from other organisms by Sarah Williams in Science

 Here is the full text of my responses:

---

"got asked by another reporter to comment on this

so - have seen the paper 

it is interesting .. but I am not overwhelmed by what they present in the paper itself. For example, the HAS story seems really incomplete as presented (e.g., the Figure showing the tree does not have all the HAS1, HAS2, HAS3 genes even though they imply they studied that). "

---

I have been looking through the supplemental information. I find it impossible to judge the quality of this paper without being able to see the alignments they used for each phylogenetic tree. I cannot find alignments for the trees even after going to their Figshare site with the trees. I therefore think there is not much to say about the paper until being able to see those. 

Without seeing the alignments I offer multiple alternative hypothesis for their findings

1. They have identified genes for which they are unable to produce reasonable alingnments. Alignments are central to phylogenetic analysis and if their alignments are poor quality then the trees will show all sorts of anomalies that have nothing to do with phylogenetic history. By scanning through 1000s of genes and flagging those with unusual patterns they may be selectively identifying genes for which producing good alignments between species is tough. I note - clustalw is a bit notorious for not producing idea alignments in some cases.
2. I do not buy their arguments for why gene loss is not a possible explanation. They need to present more detail on how many gene losses would be required for each gene family under consideration and then present some evidence for why that # of gene losses is less likely than HGT.
3. They have not even considered as far as I can tell, the possibility of divergent evolution (as opposed to gene loss) in many taxa which could lead to them being unable to identify homologs in some species
4. I am not convinced by the arguments against long branch attraction as an explanation for some of the tree patterns.
5. Related to alignments they need to show which regions of alignments they excluded from phylo
6. Convergent evolution could also explain some of the patterns they observe.
7. I could go on. I am NOT saying that HGT into chordates is impossible. It seems plausible. But it is up to them to exclude other MORE plausible alternatives and I just do not think they have done that.

---

Reporter: asking if it was OK to quote me

Yes it is OK to quote from me. I would like to reiterate - I am not saying they are wrong. Just that I would like to see (1) all the data (e.g., alignments) that unreels their conclusions and (2) them do more to exclude other possibilities.

---

Reporter asking what other analyses could they do

So - I don't want to be difficult, but it is their job to figure out how to do such tests before claiming they have strong evidence for HGT. 

In general, this is pretty typical of claims of HGT. Many researchers show evidence that is consistent with the occurence of HGT (which they did here) but few actually explicitly test alternative hypotheses such as gene loss, bad alignments, convergence, divergence, contamination, random noise, and more. I think their work is certainly interesting, but they just have not tested all of these alternatives. And I personally have grown a bit tired of pointing out how people can do better controls for their papers.

---

Reporter asking about initial impressions:

I see little here that is particularly convincing evidence for HGT ...

---

My follow up email

Note - I am not saying that this is a bad paper -- just that I am not overwhelmed by their evidence and especially by what they put in the paper. 

For example, the HAS1 gene story seems incomplete.  Figure 3 seems to show just HAS1 but in the text the say they show the same thing for all HAS genes.  And the tree they show shows a tiny subset of all the available sequences (e.g., HAS1 HAS2 HAS3 and fungal and bacterial homologs).  They claim that they now have proof that HAS1 was transferred near the base of chordates but I just don't see how they tested alternative hypotheses ...

---

Some related links:

• Bacterial DNA in Human Genomes | The Scientist Magazine®
• Researchers Challenge Recent Claim That Humans Acquired 223 Bacterial Genes During Evolution
• Slideshare of slides from talk where I discuss this topic a bit

Also here are some presentations from many years ago with some discussion of HGT

Phylogenomics - talk by J. Eisen in 2000 at MBL Molecular Evolution Course from Jonathan Eisen

Talk by Jonathan Eisen for GSAC2000 on "Phylogenomics" from Jonathan Eisen

Probiotics for athletes? Possible someday, but right now - I (and others) don't think so

Nice article in Outside Magazine by David Despain: Should You Be Taking Probiotics? | Performance Plate | OutsideOnline.com.  The article has comments from me, Peter Turnbaugh and Ellen Silbergeld.  The article discusses some of the overhyped claims about probiotics and athletic performance and even mentions my Overselling the Microbiome award.  I like in particular the following paragraph:

The biggest issue scientists currently have with probiotics, however, doesn’t have to do with athletes. Instead, it has to do with the initial hypothesis that we need them in the first place, says Ellen Silbergeld, a professor of Johns Hopkins Bloomberg School of Public Health. Because there’s still no real understanding of what makes “healthy” or “poor” microbiomes, there’s no real understanding of how or if we should cultivate them.

Today's gender biased meeting-GlycoCom2015-sponsored by @generalelectric @ualberta #YAMMM

Got pointed to this via a Tweet:

@phylogenomics yet another ... http://t.co/lNCJJ6CiLo
— Lewis-X Research (@Lewis_Lab) March 8, 2015

The Tweet pointed to this meeting: Home - Glycomics Official Website of GlycoCom Conference 2015 in Banff, Alberta, Canada.  Lame.  14:1 ratio of men: women speakers.  Just completewly lame.

Confirmed Speakers

• Richard Cummings, Emory University School of Medicine
• Paul DeAngelis, University of Oklahoma and Caisson Biotech LLC
• Donald Jarvis, University of Wyoming and GlycoBac LLC
• Nicole Koropatkin, University of Michigan Medical School
• Mario Feldman, Washington University, St. Louis and VaxAlta Inc.
• Gordon Lauc, University of Zagreb
• Todd Lowary, Alberta Glycomics Centre and University of Alberta
• John Magnani, GlycoMimetics Inc.
• Glenn Prestwich, University of Utah and GlycoMira Therapeutics Inc.
• Peter Seeberger, Max Plank Institute
• Tadashi Suzuki, RIKEN Global Research Cluster
• Ajit Varki, University of California, San Diego
• David Vocadlo, Simon Fraser University and Alectos Therapeutics Inc.
• Michael Wacker, GlycoVaxyn AG
• Robert Woods, Complex Carbohydrate Research Center & Glycosensors & Diagnostics, LLC

The University of Alberta and GE and the other sponsors should be embarassed by this.  

My microbiome talk at #FOGM15 - the perils (and fun I guess) of redoing one's talk at the last minute

Just got back from the Future of Genomic Medicine 2015 meeting where I gave a talk about microbiomes.  My original plan was to talk about the need for evolutionary and ecological approaches to microbiome studies but I changed my mind a few days before the meeting and decided to switch to talking more about citizen microbiology.  I did this because the meeting has a lot of people who think about digital and wearable technology and public engagement in the audience and it just seemed like a good chance to introduce them to the growing personal/citizen microbiology movement.

To help prep for my talk I emailed some colleagues who work on Citizen Microbiology (including a few in my lab like Jenna Lang and David Coil) and asked them if they had any slides I could pilfer.  And then I started drafting an outline of my talk (I draft all my talks by hand with pen and paper). Here are my handwritten notes

 I realized I would not likely be able to focus enough at home to work on the talk so I kind of waited until heading down to San Diego on Wednesday (talk was on Friday).

I got in pretty late and worked a little on my talk before going to bed.  I also emailed the organizers of the meeting to say I was changing the topic of my talk a bit and asked if they could change the online program which they did.  Eric Topol in response to my saying I wanted to talk about citizen microbiology and personal microbiomes very wisely suggested that I talk about my vision for the future of microbiome research.  I (lamely) had been so focused on Citizen Microbiology that I had not been thinking much about the bigger picture.  But once he suggested this notion my talk really congealed (in my head and on paper at least).  It is interesting to me how one simple suggestion from someone with vision and perspective can transform one's thought process so much ...

Anyway, the next day I headed over to the meeting venue (by the beach - life is rough in San Diego).  I got there in time to hear Francis Collins' talk.  I spent the day sitting outside in the outdoor tent viewing area, pondering my talk and listening to the talks of others. Lots and lots of interesting things presented there.  More about this later I hope.  Anyway - that evening I worked on my talk some more, headed down to the hotel bar for a bit and then worked on my talk some more.  And eventually went to sleep.  Friday I spent much of the AM working on my talk in the outdoor tent (while listening to the talks though this time not watching them on the screen since I was a bit too far away from it).  And voila - only 30 minutes before the PM session was to begin I finished the prep.  I do not like to do this normally but I just felt like my talk would be much better if I re-conceived it and I had to make all new slides pretty much for the whole talk (other than the few I pilfered from colleagues).

I note - I was talking after Marty Blaser and figured I would not have to introduce the human microbiome at all and also that he would give an overview of the risks that come from disturbing the microbiome.  Anyway, I gave my talk, and recorded the slideshow with Camtasia.  Below are my slides, the video slideshow, and a Storify of the Tweets others posted during my talk.
As is frequently the case, afterwards I felt I was too rushed and that it was not the best talk I have ever given. But that being said, I like the general outline and some of the concepts and figured I should share, warts and all. My biggest regret after talks which I have rushed a bit in preparing is that I usually do not do a great job in mentioning who did all the work I refer to. I try to put people's pictures and names on all slides and references but I don't always get this done in time and I worry I screwed this up for a few topics here. Oh well, life goes on ...

Here is a slideshow with Audio (which I recorded via Camtasia)



Here is the Slideshare posting of my slides

Talk for #FOGM15: Challenges and Opportunities in Microbiome Studies and the Rise of Citizen Microbiology from Jonathan Eisen

Today's YAMMM - The British Society for Plant Pathology

Well, this is not the most egregious example of a mostly male meeting but it still has some issues: The BSPP - The British Society for Plant Pathology 2015 meeting.  Nine speakers.  Seven male.  And this in a field with plenty of excellent female researchers.

Cassava brown streak disease
(1) James Legg - IITA Tanzania
(2) Stephan Winter - Leibniz Institute DSMZ Germany
(3) Maruthi Gowda - Natural Resources Institute, University of Greenwich

Late blight
(1) Bill Fry - Cornell University
(2) Sophien Kamoun - Sainsbury Lab, Norwich
(3) Jonathan Jones - Sainsbury Lab, Norwich

Rice blast
(1) Sarah Gurr - University of Exeter
(2) Lauren Ryder - University of Exeter
(3) Thomas Kroj - INRA, Montpellier, France

But the weirdest part --  it says

"This year, the BSPP President, Prof. Gary Foster, has only chosen a few invited speakers on specific diseases, and wishes the remainder of the talks to be selected from offered papers."

So does this mean Prof. Gary Foster just picked all speakers?  If so, perhaps Prof. Gary Foster needs to do a little thinking about his possible biases ...

Another day, another microbiome journal ... alas not as "open access" as claimed

Just got this email

Dear Doctor Jonathan Eisen,

I would like to invite you to consider submitting a paper to our recently launched Open Access journal Microbiome Science and Medicine (http://www.degruyter.com/view/j/micsm).
As can be seen from the titles of articles published in our first volume, MICSM reflects the full breadth of research in the diverse areas of microbiome-related science, from molecules to ecosystems:
Newton ILG, Sheehan KB, Lee FJ, Horton MA, Hicks RD "Invertebrate systems for hypothesis-driven microbiome research"
Amato KR "Co-evolution in context: The importance of studying gut microbiomes in wild animals"
Nelson DR, Tu ZJ, Lefebvre PA "Heterococcus sp. DN1 draft genome: focus on cold tolerance and lipid production"
Rudlaff RM, Waters CM "What is the role of cyclic di-GMP signaling within the human gut microbiome?"
Fang Y, Chia N, Mazur M, Pettigrew J, Schook LB, White BA "Genetically identical co-housed pigs as models for dietary studies of gut microbiomes"
MICSM is a broad-spectrum platform for the rapid publication of works of broad significance, originality and relevance in all areas related to the study of microbiomes, their components, and their roles in health and disease. We solicit research and review articles, as well as communications and vision papers. The manuscripts submitted in response to this invitation will be processed with the highest priority and all accepted papers will be immediately available on-line.

Authors are offered a variety of benefits:
– transparent, comprehensive and fast peer review;
– language assistance for authors from non-English speaking regions;
– convenient, web-based manuscript submission and tracking system;
– efficient route to fast-track publication and full advantage of De Gruyter Open's e-technology;
– no publication charge in the first two annual volumes.

I look forward to your manuscript!
Please forward this invitation to any interested colleagues and associates.

Seemed right up my alley - an open access microbiome journal.  Alas, when I clicked on the journal link and then browsed around I found out that articles will be published using some pretty restrictive conditions. Some key parts of the text from this page is below:

1. License
The non-commercial use of the article will be governed by the Creative Commons Attribution-NonCommercial-NoDerivs license as currently displayed on http://creativecommons.org/licenses/by-nc-nd/3.0/., except that sections 2 through 8 below will apply in this respect and prevail over all conflicting provisions of such license model. Without prejudice to the foregoing, the author hereby grants the Journal Owner the exclusive license for commercial use of the article (for U.S. government employees: to the extent transferable) according to section 2 below, and sections 4 through 9 below, throughout the world, in any form, in any language, for the full term of copyright, effective upon acceptance for publication.

Other than being, well, painfully legalesy, this is just too restrictive for me and does not really seem like "open access".  The no derivatives part drives me batty.  Also they write:

9. Scope of the Commercial License
The exclusive right and license granted under this agreement to the Journal Owner for commercial use is as follows:
 to prepare, reproduce, manufacture, publish, distribute, exhibit, advertise, promote, license and sub-license printed and electronic copies of the article, through the Internet and other means of data transmission now known or later to be developed; the foregoing will include abstracts, bibliographic information, illustrations, pictures, indexes and subject headings and other proprietary materials contained in the article,
 to exercise, license, and sub-license others to exercise subsidiary and other rights in the article, including the right to photocopy, scan or reproduce copies thereof, to reproduce excerpts from the article in other works, and to reproduce copies of the article as part of compilations with other works, including collections of materials made for use in classes for instructional purposes, customized works, electronic databases, document delivery, and other information services, and publish, distribute, exhibit and license the same.
Where this agreement refers to a license granted to Journal Owner in this agreement as exclusive, the author commits not only to refrain from granting such license to a third party but also to refrain from exercising the right that is the subject of such license otherwise than by performing this agreement.

Well, no thanks.  Too many restrictions and not open access in my view.  If I had to choose a "microbiome" journal to publish in, I would choose "Microbiome" an actually open access journal, where papers have the following info on them:

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Go Microbiome ...

Today's all male genomics meeting brought to you by Oxford Nanopores

The Tweets about this really say it all so I am just going to embed them here:

Disappointed that 9/9 speakers lined up for @nanopore’s MinION conference are men http://t.co/UJ8gSy32Rn #YAMMM cc @phylogenomics @hollybik

— Karen James (@kejames) February 25, 2015

@kejames Was it renamed ManIon conference? @nanopore @phylogenomics @hollybik

— Claudia Taake (@ct_la) February 25, 2015

@kejames @nanopore @phylogenomics @hollybik However, close to 100% of the attendees are woman, according to picture 1.

— Nicolas Robine (@notSoJunkDNA) February 25, 2015

@notSoJunkDNA Yeah, I noticed that. Odd choice, considering. @nanopore @phylogenomics @hollybik

— Karen James (@kejames) February 25, 2015

Really disappointed in Oxford Nanopores.  Perhaps we can get some of the speakers to cancel on them unless they fix things.

• Ron Ammar, University of Toronto, Canada
• Ewan Birney, European Bioinformatics Institute, UK
• Thomas Hoenen, NIH/NIAID, USA
• Nick Loman, University of Birmingham, UK
• Brook Milligan, New Mexico State University, USA
• Justin O’Grady, University of East Anglia, UK
• Jared Simpson, Ontario Institute for Cancer Research, Canada
• Yutaka Suzuki, University of Tokyo, Japan
• Mick Watson, The Roslin Institute, University of Edinburgh, UK

Update 3/8/15 

Well, after I posted about the Nanopore meeting there were some responses on Twitter. So I made a Storify

So I decided to check the meeting today to see whether they "fixed" anything.

Right now they list 11 male and two female speakers.  So that added two males and two females.  Better ratio.  Still pretty bad.  They really could do better ...

Oxford Global Sequencing Meetings: Where MEN Tell You About Sequencing #YAMMM

Well, got an email invite to one of these Oxford Global Meetings. Sadly the gender ratio of listed speakers is awful. I highlighted the list below (men in yellow, women in green).  Ratio of 17:3.  (See below).  No thanks Oxford Global.

Dear Professor Jonathan Eisen ,
 We hope you are well and we would like to invite you to speak at our forthcoming Next Generation Sequencing (NGS) USA congress (www.nextgenerationsequencingusa-congress.com) or co-located  Single Cell Analysis USA congress (www.singlecellusa-congress.com) to be held on 27th -28th October 2015 at Harvard Medical School, Boston, USA.
 Over the two days, the NGS USA congress aims to cover updates and application of NGS technologies in genomics and genetics research in the US and UK, Europe. Topics are comprised of NGS & NGS Data Analysis Technologies and Platforms, NGS for Cancer Drug Development, Microbiology and Immunotherapy as well as Clinical Applications & Diagnostics. Novel updates in Gene Synthesis, Protein Sequencing and Targeted Sequencing will also be explored The Single Cell Analysis USA congress looks at new methods in DNA sequencing, epigenomic DNA sequencing and RNA sequencing, informatics, data handling as well as application of single cell genomics in understanding cancer  other areas of cancer research such as cancer stem cells and immunotherapy. The presentations are also comprised of novel techniques in imaging and cytometry, isolation and processing of single cells. The congress also covers the applications in translational medicine and the clinic for therapeutic targeting.
 The combination of carefully researched topics and high-level networking opportunities creates a unique discussion platform for over 250 senior scientists we are expecting in attendance from research institutions and pharmaceutical companies. Confirmed Speakers for 2015 include:NGS·          Sreekumar Kodangattil, Senior Principal Scientist, Pfizer       
·          Shrikant M. Mane, Senior Research Scientist in Genetics; Director, MBB Keck Biotech laboratory; Director, Yale Center for Genome Analysis
·          Stephan Schuster, Professor of Biochemistry and Molecular Biology, Penn State University
·          Richard  McCombie, Professor, Human Genetics, Cold Spring Harbor Laboratory
·          Jingyue  Ju, Director, Center for Genome Technology and Biomolecular Engineering, Professor of Chemical Engineering and Pharmacology, Columbia University            
·          Christopher Mason, Chair, ABRF NGS Consortium, Assistant Professor, Weill Cornell Medical College. Dept. of Physiology & Biophysics; The Brain & Mind Research Institute
·          Michaela Bowden, Associate Director, Center for Molecular Oncologic Pathology, Dana Farber Cancer Institute      
·          Yuan Gao, Director, Associate Professor, Lieber Institute/Johns Hopkins University
·          Sheng Li, Instructor in Bioinformatics, Department of Neurological Surgery, Weill Cornell Medical College
·          Michael  Fraser, Associate Director, CPC-GENE Prostate Cancer Genomics Program, Princess Margaret Cancer Centre    
 Single Cell·          Daniel Chiu, Professor, University of Washington    
·          Steve Potter, Professor, Division of Developmental Biology, Cincinnati Children's Medical Center
·          Norman Dovichi, Professor, University Notre Dame 
·          Zaida Luthey-Schulten, Professor of Chemistry, University of Illinois
·          Paul Bohn, Professor of Chemical and Biomolecular Engineering, University of Notre Dame       
·          Navin Varadarajan, Assistant Professor, University of Houston
·          Alexander R., Ivanov, Director of the HSPH Proteomics Resource, Research Scientist
Harvard School of Public Health·          Viktor Adalsteinsson, Researcher, Researcher, Koch Institute at MIT, Broad Institute of MIT and Harvard Medical School
·          Xinghua Victor Pan, Research Scientist, Single Cell Genomics Group, Sherman Weissman Laboratory, Department of Genetics, Yale University School of Medicine
·          Cheng-Zhong Zhang, Computational Biologist, Department of Medical Oncology, Dana-Farber Cancer Institute

Two Eisen lab papers selected for the PeerJ 2015 Collection

Cool.  Two paper from my lab were selected as highlights of 2014 papers in the Peer J: PeerJ Collection: PeerJ Picks 2015 Collection

The papers were

The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types

Jenna M. Lang,  Jonathan A. Eisen,  Angela M. Zivkovic

and 

PhyloSift: phylogenetic analysis of genomes and metagenomes

Aaron E. Darling,  Guillaume Jospin,  Eric Lowe,  Frederick A. Matsen,  Holly M. Bik,  Jonathan A. Eisen

Thanks PeerJ and all the co-authors for their great work.  I love open science and I particularly think we need continuing experiments on the best ways to do open science.  Thus I like the experiment that is PeerJ in regard to how to publish and how to pay for open access fees.

Full disclosure: I am an Academic Editor at PeerJ.

Overselling the microbiome award: CBC Fresh Air & JA Tetro on kissing microbiomes

Well, so there I was, enjoying a relatively peaceful and quiet Valnetine's day.  When I noticed a Tweet directed to me from one of my favorite scientist's out there

@phylogenomics Please help stop this "bacteria determine who we like" and "Germs Relational Expert"BS. https://t.co/70yDKM5Gf9
— Elisabeth Bik (@MicrobiomDigest) February 14, 2015

So I decided to check it out.  I clicked on the link and got to a CBC Fresh Air news story on Soundcloud:

▶ Kissing and romance and bacteria with Jason Tetro Feb 14/15 by CBC Fresh Air

I plugged in my headphones (was not sure if my kids should hear it) and listened away.  And what I heard was excrutiatingly painful.  The CBC Fresh Air reporter was discussing kissing and the microbiome with JA Tetro.  And Tetro made some of the most misleading, ridiculous overstatements about the microbiome I have heard in many years:

• He basically implied or specifically said that, in humans, attraction to partners and relationship success was determined by finding a partner with similar microbiomes to oneself.  
• Furthermore he discussed how maintaining similar microbiomes (e.g., via consuming the same probiotics or fermented foods) would help maintain attraction and how things like travel away from a partner might lead to repulsion.  
• He said things like tha our immune systems determine if a partner is right for you from kiss-based comparison of a partner's microbiome to one's own.  
• And that if the microbiome in a kissing partner is a match this leads to bliss and addiction and that salive is the first line of defense when it comes to relationships.  
• He even went so far as to say that this is all about "trying to find your mother because our microbiomes come from our mother."  

I could do on and on.  It was the worst, most misleading, innacurate material I have probably ever heard about microbiomes.  Tetro and CBC Fresh Air should be ashamed.

Sadly, I found some other misleading, inaccurate material from Tetro about the same topic in an article about kissing microbiomes from a few months ago: Swapping spit and testing chemistry: How kissing, germs help you pick your partner where Tetro is quoted

Tetro says that when you kiss your date, his or her germs make their way into your mouth’s ecosystem. And if it’s a match, you’ll want to keep smooching. 

“This study does one amazing thing, it shows you that kissing is the best way to find a mate for the long term. It might sound really gross but if the bacteria from the other person harmonizes with your bacteria, your immune system is all good. You feel a sense of calm and happiness, maybe even addiction,” he explained. 

“But if the bacteria don’t align with your microbes, you actually feel disgust and revolt. Your immune system is rejecting that person as a possible mate.”

and

“This study proves that when it comes to finding the right mate, the old game of spin the bottle actually has a base in science,” he said. 

More completely inaccurate, made up material with no basis in science.  As far as I can tell, this is basically made up.  Sure there may be a theory behind this.  But to present it as established facts about the microbiome is ridiculous.

This is all a shame really since the paper which the CBC Fresh Air story is referring to is actually a perfectly fine paper and the authors of the paper do not seem to be pushing these over the top ridiculous ideas.  And for this terrible story I am giving CBC Fresh Air and JA Tetro an "Overselling the microbiome award".

Twisted tree of life award: throwback PR from an ingrained Oregon State

Just got pointed to this PR:  Unwanted impact of antibiotics broader, more complex than previously known -- ScienceDaily

It has one of the worst microbe-evolution sections of text I have seen in a long long time:

Mitochondria plays a major role in cell signaling, growth and energy production, and for good health they need to function properly. 

But the relationship of antibiotics to mitochondria may go back a long way. In evolution, mitochondria descended from bacteria, which were some of the earliest life forms, and different bacteria competed with each other for survival. That an antibiotic would still selectively attack the portion of a cell that most closely resembles bacteria may be a throwback to that ingrained sense of competition and the very evolution of life.

Yup.  That antibiotics that target bacteria also affect mitochondria is a throwback to that ingrained sense of competition and the very evolution of life. 

Can anyone - anyone - please - please - tell me what that means?

For this, I am giving the folks from Oregon State a coveted Twisted Tree of Life Award.

Another "Yet another mostly male meeting (YAMMM)" from BGI

Well just saw an announcement for this meeting on Twitter: The First Announcement of The Tenth Annual Meeting of the International Conference on Genomics (ICG

And I hoped beyond hope that they would have a decent representation of women speakers at the meeting.  Why did I hope this?  Well, in the past, BGI run meetings have had incredibly skewed gender ratios of speakers.  See this post for a discussion of their past record: Kudos to the DOE-JGI for organizing a genomics meeting w/ a good gender ratio - no kudos to BGI - yet again

I guess I had hoped that perhaps they would try to change their practices after I and other people criticized them for their past record.  So - I went to the web site for the ICG10 meeting advertised in the Tweet.  Oh well, silly me for hoping.

On the front page they have 14 speakers they are promoting - all of them male.

Screen shot from ICG10 web site

On the announcement page they have a slightly different list where the ratio is 14:1

• Jef Boeke, NYU Langone University School of Medicine, USA
• Sydney Brenner, 2002 Nobel Laureate in Physiology or Medicine, Singapore
• Charles Cantor, Sequenom, Inc., USA
• Julio Celis, Danish Cancer Society Research Center, Denmark
• Richard Durbin, Wellcome Trust Sanger Institute, UK
• Leroy Hood, Institute for Systems Biology, USA
• Thomas Hudson, Ontario Institute for Cancer Research, Canada
• Maria Leptin, Chair of EMBO, Germany
• Maynard Olson, University of Washington, USA
• Aristides Patrinos, J. Craig Venter Institute, USA
• Mu-ming Poo, University of California, Berkeley, USA
• Richard Roberts, New England Biolabs, 1993 Nobel Laureate in Physiology or Medicine, USA
• Eils Roland, Heidelberg University, Germany
• Mathias Uhlen, Royal Institute of Technology, Sweden
• Tilhuan Yilma, University of California, Davis, USA

Regardless, this is a consistent pattern of not having an even remotely balanced ratio of male to female speakers at their meetings.  And please, avoid their meetings until they change this.

Science based decision making in education: sleep and school start times in #DavisCA and beyond

In September of last year I wrote a brief post about science and decision making in schools: Nice letter to the editor in the Davis Enterprise taking on school district's anti-science tone.  I include it below since it is very relevant to this post.

----------------------------------
I assume many people heard about the recently released report from the American Academy of Pediatrics where they recommended high school classes start later in the morning than most do right now.  See for example: Let Them Sleep: AAP Recommends Delaying Start Times of Middle and High Schools to Combat Teen Sleep Deprivation.  And this report was covered in all sorts of newsy and bloggy places.   See for example, Amy Graff's article in SFGate and Deborah Netburn in the LA Times.  Overall, the argument presented by the AAP makes sense and seems supported by scientific fundings.  And they go through a lot of scientific reasons for their recommendations.

Alas, Winfred Roberson, superintendant of the Davis, CA schools (also known as the DJUSD) told the Davis Enterprise that the schools here would not be making any changes in response to this report:

“While DJUSD won’t be modifying start times, our role as an educational institution can be to find ways to support our students by giving them the tools that will help them to think through, make adjustments and prioritize their competing forces that may be cutting into the recommended sleep time,” Roberson said. “These are life skills we are helping to build that will help students to function even after graduation.”

And I had missed out on this quote, thankfully, but became aware of it when my wife showed me this letter by Steve Carlip in the Davis Enterprise today:  Don’t ignore the science Davis Enterprise.   I quote from it below:

The superintendent’s response, as reported in Tuesday’s Enterprise, was to simply ignore the science. Instead, he said, the schools will help student “build life skills” to “prioritize their competing forces that may be cutting into the recommended sleep time.” 

Really? The high school is going to teach students to control their circadian rhythms? It’s going to give them the “life skills” to regulate the timing of their bodies’ secretion of melatonin? It will educate them to overcome biological sleep-wake phase delay by sheer force of will?

He completely nailed it here.  I hope Winfred Roberson and the Davis School district rethink their attitude towards scientific studies.
-----------------------------------

Today I found out that the Davis School Board may actually be listening to the science.  For the next school board meeting which is February 5 there is an agenda item on this topic c. Update on the Formation of a DJUSD Sleep Study Committee. The description of the agenda item is as follows:

In August 2014, the American Academy of Pediatrics released a scientific sleep study report that recommended an 8:30 am start time for schools, which would allow secondary students more time to sleep.  The report generated community discussions and concerns since Davis secondary schools start before 8:30 am.
In response, the superintendent initiated the formation of a Sleep Study Committee (made up of students, teachers, counselors, parent/community members and administrators) to examine the benefits and logistical challenges of an earlier school start.    

This update is a report of the formation of the Sleep Study Committee and their charge.  For reiteration, at this time, staff is not offering recommendations about a modified start time.  Staff will wait to review the work of the Sleep Study Committee before offering formal recommendations to the Board. 

So I started digging around for more on the topic and found some things worth reading  But the most interesting thing I found was that there has been a discussion about this exact issue in the county where I grew up: Montgomery County Maryland.  Some of the articles about this area listed below:

• Washington Post 1/23/15: Montgomery parents plead for later high school start times
• Sentinel 1/27/15: Parents voice overwhelming support for delaying high school start times
• Bethesda Magazine: Parents, Medical Professionals Push for Later School Start Times in Montgomery County ...

It seems to me that Davis, CA really needs to consider this as a possibility.  It could help students in many ways and seems to be a relatively easy (though not free of course) way to improve the lives and learning of students in our town.  I am thrilled that the Board is bringing the topic up again.  Any examples out there of places that have shifted start times based on the AAP recommendation would be great (and what happened ...). 

See some responses on Twitter:

Heay @DavisVanguard - have you ever written about the "start school later" issue / topic? (e.g., see http://t.co/pAGnhUUUeP)
— Jonathan Eisen (@phylogenomics) February 2, 2015

@phylogenomics weird.. Anyway, I was on later start time task force in Albany CA. V. successful move to 815 start time for HS.

— Matt MacManes (@PeroMHC) February 3, 2015

@phylogenomics reduced tardiness, better performance in 1st period. Teachers and parents love it - though was initially a tough sell.

— Matt MacManes (@PeroMHC) February 3, 2015

Best post doc position ever: w/ Jessica Green, myself, Jay Stachowicz, Jenna Lang

copied from U. Oregon web site

Postdoctoral Research Scholar
Institute of Ecology and Evolution

Posting: 14431
Location: Eugene
Closes: Open Until Filled

Revised Posting
Postdoctoral Position in Microbial Ecology and Evolution
Jessica Green at the University of Oregon (http://pages.uoregon.edu/green/) is currently seeking a postdoctoral researcher to collaborate on the Seagrass Microbiome Project (http://seagrassmicrobiome.org).  

Applicants should have a Ph.D. in a biological, computational, mathematical, or statistical field and strong writing skills.  The ideal candidate will have experience developing and applying models to understand the ecology, evolution, and/or function of complex systems.  Experience in the analysis of environmental sequence data is highly desirable, but not required. 
  
The successful candidate will have the opportunity to creatively and independently tackle one or more of the science questions outlined in the Seagrass Microbiome Project grant proposal (http://seagrassmicrobiome.org/2014-grant-proposal/), funded by the Gordon and Betty Moore Foundation.  

The successful candidate will interact regularly with team members Jonathan Eisen (http://phylogenomics.wordpress.com), Jay Stachowicz http://www-eve.ucdavis.edu/stachowicz/stachowicz.shtml, and Jenna Lang (http://jennomics.com/) at the University of California, Davis through weekly tele-conferencing and also through regular visits to the UC Davis campus. 

At the University of Oregon, the candidate will benefit from ongoing microbiome research programs including the Microbial Ecology and Theory of Animals Center for Systems Biology (http://meta.uoregon.edu/) and the Biology and Built Environment Center (http://biobe.uoregon.edu/).

The position is available for 1 year with the possibility for renewal depending on performance.  The start date is flexible.  Please email questions regarding the position to Jessica Green (jlgreen@uoregon.edu).

To apply
A complete application will consist of the following materials:
(1) a brief cover letter explaining your background and career interests
(2) CV (including publications)
(3) names and contact information for three references 
Submit materials to ie2jobs@uoregon.edu.  Subject: Posting 14431

To ensure consideration, please submit applications by March 10, 2015, but the position will remain open until filled. Women and minorities encouraged to apply.  We invite applications from qualified candidates who share our commitment to diversity. The University of Oregon is an equal opportunity, affirmative action institution committed to cultural diversity and compliance with the ADA. The University encourages all qualified individuals to apply, and does not discriminate on the basis of any protected status, including veteran and disability status.

Office of Affirmative Action & Equal Opportunity · 677 East 12th Ave., Suite 452 · 5221 University of 

Oregon, Eugene, OR 97403-5221 Office (541) 346-3123, Fax (541) 346-4168 · This announcement is

 available in alternate formats upon request.  If you are a qualified applicant with a disability and need 

accommodation with the application process, please contact us for assistance.