Wrap up of recent posts of relevance on microBEnet

I have been doing a lot of blogging at microBEnet and don't always do a good job of cross posting or even posting here to let people know of the cross talk / related posts.

So I am trying to do that briefly now.  Here are some posts from the last few months on microBEnet that may be of interest, These are posts from March through today.

• Great article by Maryn McKenna on the hunt for new antibiotics w/ crowdsourcing help
• Worth a look: Are Pets the New Probiotic? in the NY Times
• Alleged mishandling of Flint Legionnaire’s outbreak leads to manslaughter charges for MI health chief
• Report: Guests leave Las Vegas’ Rio hotel with Legionnaires’ disease
• A hairy pacman approach to “microbial dark matter” in drinking water
• Pre-microbiology – Ancient Imaginations of the Microbial World
• New paper of interest on antibiotic resistance genes in 4 CA cities but dangerous PR from UCLA
• Compiling a list of Microbiology of the Built Environment related presentations at ASMicrobe17
• Love the #AgarArt contest from ASM …
• Dirty money: interesting data but unclear what implications are
• Who are the microbes in your neighborhood? In your neighborhood? In your neighborhood?
• A fascinating side story to brain-defect microbiome study – major role of the built environment
• Kristen DeAngelis slides for “Microbial Diversity” Course
• Why use Bracken instead of Kraken?
• This is calling out for a large microbiome study: Salt from icy roads is contaminating North America’s lakes
• Your help is wanted in this #CitizenMicrobiology project: “BashTheBug – Help us fight antibiotic resistance!”
• Dr. Director & Duflo: Dogs Dropping Doody Do Digestive DNA Data Duty 
• Day 2 of #NeLLi17: From New Lineages of Life To New Functions
• Interesting discussion of data vs. metadata started at #NeLLi17 & continuing
• Day 1 of #NeLLi17 – From New Lineages of Life To New Functions 
• Journal of Bacteriology minireview collection on host-microbe interactions
• Paper of interest comparing taxonomies of SILVA, RDP, Greengenes, NCBI and OTT 
• Are ‘germ-zapping’ robots useful in fighting hospital acquired infections?
• Wanted – help compiling a list of academic #microbiome centers
• Quick post – this looks potentially very useful – ATLAS – comprehensive infrastructure for assembly, annotation, & genomic binning of metagenomic data 
• Reasonably cautious but optimistic editorial on “The human microbiome: an emerging tool in forensics” 
• The microbiomes of built environments when the builder is not human
• 
  

Irresponsible reporting on "poop doping" from the Washington Post

UPDATE 1 - see below - the author updated her article including some of my critiques.
UPDATE 2 - also see Embryette Hyde's post about using (or not using) the American Gut data to inform lifestyle changes
UPDATE 3. June 25. - Boing Boing picked up the story.  Without major caveats.  I posted a comment there pointing to my blog and answered one other comment but then was not aware the discussion was going on much more there until a Tweet today.  Some interesting discussions there and also some strange things.  Some criticisms of me (some reasonable .. some a bit much).
UPDATE 4. June 26. Nicholas Starapoli at the Genetic Literacy Project critiques the stories on poop doping. Poop doping: No, elite athletes can’t improve performance by optimizing gut bacteria
UPDATE 5. Also see Beth Skwarecki Sex, Poop, and Champagne Are Great, But Their Health Benefits Are Overrated

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Went on a bit of a Twitter tirade last night. See more below



The Washington Post story, by Marissa Payne, requires a log in but the article is now in other papers that are free online including the Denver Post here.

It is just really bad reporting because the claims of one scientist are presented as facts without any scrutiny and these claims need lots of scrutiny.

Recently this story was covered in Bicycling Magazine and I gave them an "overselling the microbiome" award for their reporting on it.  I guess I am pretty surprised that the Washington Post doubled down on some of the claims.

Here is some commentary on just some of what is wrong with the Post article.

"Peterson, herself a pro endurance mountain biker, has discovered that the most elite athletes in the sport have a certain microbiome living in their intestines that allow them to perform better"

No evidence has been presented anywhere that these microbes "allow them to perform better".  At best, there may be evidence that elite athletes in this case have different microbes.   That as far as I know has not been presented for the case here.  Seems possible.  But this of course does not mean that those microbes they have allow for better performance.  There could be dozens of reasons why such athletes have differences in their micro biomes (e.g., diet, exercise, interactions all effect the microbiome).

Peterson didn’t decide on the fecal transplant solely to enhance her performance during her mountain bike races, but to cure a host of symptoms that have affected her since she was a child and contracted Lyme disease.

Seriously?  This basically is implying that she did a self fecal transplant that enhanced her performance and cured her Lyme disease.  She is an N of 1.  She did a fecal transplant and then some of her self assessed health changed.  What about, say, the placebo effect?  Or, how about - 100 other things changed in her life before and after the fecal transplant which could have affected her.  Or maybe the antibiotics she claimed to have taken before the transplant did something?  Ridiculous to make any claims about her self fecal transplant having any known impact.

Then there is this

“I had no microbes to help me break down food, and I had picked up bugs in the lab where I was working because my system was so weak and susceptible,” she told Bicycling.

This is a pretty stunning claim. She had no microbes that help break down food before this?  And she also had been infected by microbes from the lab where she worked?  I don't buy either of these claims.

And what about

“I just did it at home,” she said of the February 2014 procedure. “It’s not fun, but it’s pretty basic.”

Referring to home fecal transplants.  I mean, I am all for people doing really whatever they want at home.  But they should do it with their eyes as wide open as their other parts.  And that requires the full poop on fecal transplants.  They have real and potential risks (e.g., see this).  One can get pathogens from them.  The transplant itself could have negative effects.  And if one assumes the microbiome has major effects, then one might get other unwanted traits from the donor too.  It is dangerous to promote self fecal transplants without discussing any of the possible risks.

Overall, I find this reporting by the Post to be dangerous.  And no the one caveat in the article below is not enough

Peterson said it’s too early to make any concrete conclusions about how the microbiome affects performance, but she’s convinced there’s enough evidence to suggest it does make a difference.

How about instead of "she is not convinced" saying "There is no evidence for any of her claims and this is snake oil".  That would be more accurate.

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UPDATE June 21 2:54 PM

Marissa Payne updated her story with some comments from me

See https://twitter.com/MarissaPayne/status/877631691883298816

Because the text has been changed in the Washington Post story I am posting the text here from the Denver Post version in case it gets updated too, so people can see the original.

-------------------------------
To be a professional cyclist, one must have guts, microbiologist Lauren Peterson says, and she doesn’t just mean that in the metaphorical sense. Peterson, herself a pro endurance mountain biker, has discovered that the most elite athletes in the sport have a certain microbiome living in their intestines that allow them to perform better, and if you don’t have it, well, there may soon be a way to get it.

“Call it poop doping if you must,” Peterson told Bicycling magazine last week about her research.

Peterson, a research scientist at the Jackson Laboratory for Genomic Medicine in Farmington, Connecticut, heads up an initiative called the Athlete Microbiome Project, in which she compares stool samples of elite cyclists to amateur bikers. Her findings strikingly shine a light on a handful of microorganisms that apparently separate the guts of elite athletes from average people.

The most important, perhaps, is Prevotella. Not typically found in American and European gut microbiomes, Prevotella is thought to play a role in enhancing muscle recovery.

“In my sampling, only half of cyclists have Prevotella, but top racers always have it,” she told Bicycling. “It’s not even in 10 percent of non-athletes.”

Peterson reports she hosts Prevotella in her own gut – but not naturally. In fact, she might be the first case of “poop doping,” thanks to a fecal transplant she administered herself three years ago. Her donor? Another elite athlete.

Peterson didn’t decide on the fecal transplant solely to enhance her performance during her mountain bike races, but to cure a host of symptoms that have affected her since she was a child and contracted Lyme disease.

“I had no microbes to help me break down food, and I had picked up bugs in the lab where I was working because my system was so weak and susceptible,” she told Bicycling.

But, she continued, “I couldn’t find a doctor who could help me” since in the United States, fecal transplants are only performed to treat serious cases of Clostridium difficile, a disease that causes chronic diarrhea. And so Peterson went rogue.

Peterson detailed her decision to perform the “risky” procedure on herself on the podcast “Nourish Balance Thrive” last year. She admitted to thinking it was a “bad idea” at first because if not done with proper screenings of both parties, it could worsen a person’s problems. But through chance, she came across a donor, an elite long-distance racer, who had his microbiome mapped and screened after a case of food poisoning, which showed he was otherwise healthy. So Peterson took antibiotics to wipe out her own gut bacteria and essentially performed a reverse enema.

“I just did it at home,” she said of the February 2014 procedure. “It’s not fun, but it’s pretty basic.”

Within a month, Peterson said, she began feeling better than she’d felt in years.

“I had more energy than I knew what to do with,” she told the same podcast last year. “Like everything just changed.”

More importantly for her life’s work, however, her own success with the fecal transplant gave her the idea to start the Athlete Microbiome Project, for which she rounded up 35 of her cycling friends, according to the Scientist magazine, to kick off her research.

Along with Prevotella, Peterson said she also identified another possibly performance-enhancing microbe called Methanobrevibacter archaea, which Peterson found to be more prevalent in the samples from elite athletes. This bacteria’s function is also opaque, however, Peterson told the Scientist, “it allows your entire gut microbiome to work more efficiently” by more effectively breaking down complex carbohydrates in the gut.

Peterson said it’s too early to make any concrete conclusions about how the microbiome affects performance, but she’s convinced there’s enough evidence to suggest it does make a difference.

“What we’re learning is going to change a lot for cyclists as well as the rest of the population,” Petersen told Bicycling magazine. “If you get tested and you’re missing something, maybe in three years you’ll be able to get it through a pill instead of a fecal transplant. We’ve got data that no one has ever seen before, and we’re learning a lot. And I think I can say with confidence that bacterial doping . . . is coming soon.”

Kudos to Bicycling Magazine for pedaling so so so much overselling of the microbiome

Well ... this was not a fun read.

There is an article in Bicycling Magazine by Berne Broudy and it is pretty painful to read.  The article is ​Is Poop Doping the Next Big Thing? | Bicycling.

And the answer should be "We have no $(*#()$()@#)@#  idea if this is a good idea". But instead the answer was hype, overselling, and some bad microbiology reporting.

Here are some parts I am not a fan of.

The results showed she was populated by 96% gram-negative pathogens so toxic that if they got into her blood stream they could kill her. “I had no microbes to help me break down food, and I had picked up bugs in the lab where I was working because my system was so weak and susceptible.”

I doubt much off this.  I don't think the American Gut project can say anything about pathogens nor do I think they do say this.  My guess is this is a misinterpretation by the scientist here or more likely the reporter.  Also I doubt the American Gut data could be used to say anything about picking up bugs in the lab.

She observed that Prevotella, a microorganism she received in her own transplant, is common amongst elite racers. “The more a person trains, the more likely they are to have Prevotella,” says Petersen. “In my sampling, only half of cyclists have Prevotella, but top racers always have it... it’s not even in 10% of non-athletes.”
She is currently extracting Prevotella to understand what it is, and how to boost its abundance naturally or through a probiotic pill for athletes or aspiring athletes. What she already knows: Prevotella synthesize branch chain amino acids critical for muscle recovery.

This too has some dubious parts.  Especially going from a correlation (althetes vs. Prevotella) to "how to boost its abundance."  How about first showing that is has any effect?

Archeon are ancient microorganisms that have managed to survive for millions of years in hostile habitats like sulfur springs and deep in the ocean. They also live in the human digestive system, where they have specialized functions. Like Prevotella, Elite cyclists often have M. smithii, but it’s less common in amateur racers. That’s significant because M. smithii also appears to be a performance-enhancing microbe.

Well - no modern organisms are ancient, first of all.  And no Archaea have not managed to survive for millions of years - they live and die and their lineages evolve.  As far as I know, nobody has shown this organism is performance enhancing - I could not find anything in the literature about this.  It is a nice model.  But many models are nice and then are wrong.

And then there is this

As for actual poop doping…. fecal transplants are available, but not in the U.S. “If you have the money for the procedure, you can go to a clinic in the UK or the Bahamas,” says Petersen. “But you can’t choose your donor, and it’s a risky procedure. As with any transplant, your immune system could reject what you get. It’s not something you should take lightly. I did a lot of research, and I took a risk for sure.”

Umm - she is a single case study and there is no evidence I know of that her transplant let to any improvement in performance.  Dangerous claims right here.  Fecal transplants indeed have real risks.  Encouraging people to use them for doping is dangerous.

And thus Bicycling Magazine is a recipient of the Overselling the Microbiome Award.

Wakelets summarizing Tweets about "An open digital global south meeting" at #UCDavis

I made a Storify of Tweets and some pictures from the "An open digital Global South" meeting that I am a co-organizer of. This was organized by my "ICIS project and was, to be honest, really put together by other people on the project (I helped, but definitely was not one of the major organizers). Much of the credit should go to Michael Wolfe and Alexandra Lippman. See more in the Storify below. UPDATE March 14, 2019 - replaced Storify w/ Wakelet.

Paywall the movie - trailer

Hat tip to Mackenzie Smith for pointing this out to me
Paywall The Movie Trailer from Paywall The Movie on Vimeo.

Overselling the microbiome award: Marie Claire for its "article" on Mother Dirt

Wow.  And not in a good way.  Marie Claire has bough in to the Mother Dirt sales pitch wholesale.  Here are some quotes form an article by Roxanne Adamiyatt published today in Marie Claire (see Probiotic Mist - Cleansing Body Mist)

"Like Febreze for your body, Mother Dirt's AO + Mist is a live probiotic spray that restores essential bacteria to our microbiomes. How? In short, the ammonia-oxidizing bacteria works to consume sweat on your body and turn it into a beneficial byproduct your skin can use."

Ugh.  No that is just not true.  This is what the people from Mother Dirt may claim.  But I have yet to see any evidence for this.

And then there is

"For example, if you were to use this formula on your face, the "good" bacteria in the mist would consume the ammonia (which raises pH) and restore balance to the skin i.e. it would become less sensitive, dry, or oily. And it's not just your face and body that can benefit from a reset spritz. You can use it in your hair too."

Ugh again.

And then the president of Mother Dirt is quoted

According to Jasmina Aganovic, president of Mother Dirt, it can help you go longer between washes. "The bacteria converts your sweat into byproducts your skin can use and with that, you're restoring a microorganism that once naturally existed on the scalp," she explains.

And there is more

You can also use AO+ as a quick post-workout fix as the good bacteria will consume the ammonia and urea in your sweat, AKA food for body odor. 

And

So whether it's balancing your skin, helping you prolong a blowout, or functioning as a deodorant, AO+ is working overtime to keep your hygiene in check...even if you're not. So we can't imagine something more useful to have on hand for summer.

I normally would not go the next step but I think it may be needed here - is it time to ask if Marie Claire is getting any money from Mother Dirt for this advertisement?

And for presenting the spray from Mother Dirt as proven to do things without presenting any evidence, I am giving Marie Claire a coveted Overselling the Microbiome Award.

----------------
Update: 5/1/2017 8:50 PM

But wait.  A little search of the Maria Claire web site pulled up another advertisement for Mother Dirt that is pretending to be an actual article:

Is Bacteria the Secret to Healthy Skin? by Renee Saleh in 2016.

In this article, the author basically reports on PR from Mother Dirt as though it is factual.  For example consider this:

Take acne, for example. Aganovic, who has a degree in chemical and biological engineering from MIT, has studied the presence of ammonia-oxidizing bacteria (a key component of the Mother Dirt product line) in both Western and aboriginal communities. She found that there were almost no acne cases in the aboriginal communities of Paraguay and New Guinea. These communities also shared the universal presence ammonia-oxidizing bacteria in skin cultures. In Western communities, however, acne occurs in 80 percent of adolescents, and there is less than a one percent occurrence of detectable ammonia-oxidizing bacteria on the skin. The absence of this type of bacteria in the West can be traced to the ingredients found in common household soaps and cleansers—and the decrease in time we spend in the great outdoors.

I mean.  It is a nice story.  But what is the evidence for this? None as far as I can tell.  I searched Google Scholar for papers by Aganovic on acne or aboriginal communities and found nothing.  Again, I am left wondering if Mother Dirt has paid Marie Claire for this advertising.

My one day campaign for US Senate running against my brother @senatorphd

My non supportive response to "All Biology is Computational Biology"

Round up of responses to my sign captioning request

Round up of responses to my sign captioning request

Kissing between humans and Neanderthals? Could be oral - anal contact too. Or neither.

Umm - I really do not know what to say here. There is a new incredibly exciting paper out on Neanderthal oral microbiomes.

I saw some news stories about a new study on Neanderthal oral microbiomes. And one thing caught my eye - a claim about how the data provided evidence that Neanderthal's and humans were kissing each other.
See for example the LA Times: Vegetarian Neanderthals? Extinct human relatives hid a mouthful of surprises - LA Times

The scientists also managed to sequence the oldest microbial genome yet — a bug called Methanobrevibacter oralis that has been linked to gum disease. By looking at the number of mutations in the genome, the scientists determined it was introduced to Neanderthals around 120,000 years ago — near the edge of the time period when humans and Neanderthals were interbreeding, Weyrich said 

There are a few ways to swap this microbe between species, she pointed out: by sharing food, through parental care, or through kissing. 

“We really think that this suggests that Neanderthals and humans may have had a much friendlier relationship than anyone imagined,” Weyrich said. “Certainly if they’re swapping oral microorganisms — or swapping spit — it’s not these brute, rash-type encounters that people were suspecting happened during interbreeding. It’s really kind of friendly interactions.”

And Redorbit: Neanderthals were vegetarian– and probably kissed early humans

Another surprise was the discovery of the near-complete genome for Methanobrevibacter oralis, a microbe known to live between the gums and teeth of modern humans, in the dental calculus of the Neanderthals. Weyrich said that this organism is the oldest of its kind to ever be sequenced, and that its existence in Neanderthals means that it had to have been spread to humans somehow – likely through kissing, which supports the growing notion that humans and Neanderthals were known to become intimate with one another on occasion.

And the Washington Post Neanderthal microbes reveal surprises about what they ate — and whom they kissed



And there is this doozy of a quote in the Post article

“In order to get microorganisms swapped between people you have to be kissing,” Weyrich said.

And many others.  Now - this seemed like it would be really hard to prove.  After all, it is really hard to prove from microbiome data that two people have been kissing even when we have high quality data from many samples and even when we have data from both the possible donor and recipient.  So how could one show that humans and Neanderthals were kissing with data from ancient samples and only from one of the partners in the putative exchange?  Well, as far as I can tell, you cannot.

Sadly the paper is not open access and I generally avoid writing about closed access papers here. But I am making an exception here because the media has run with what I believe to be an inaccurate representation of the science.

So I went to the paper.  Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus.  I have access to it at UC Davis but if you do not have access to it, you could search for it in SciHub (for more about SciHub see Wikipedia).  I am not encouraging you to use SciHub - a site that makes papers available view what may be illegal means in some countries.  But if you want to see the paper, and you have determined that you are OK with using SciHub, well, that is an option. This is a link that might get you access in SciHub, if you wanted to do that.

Anyway - I read the paper.  And it really is quite fascinating.  It has all sorts of interesting information and really does represent an incredible tour de force of both lab and computational work. Kudos to all involved.  But alas, there is nothing in the paper about kissing. If you search in the paper for the word kiss - it is not found. The possible transfer of microbes between Neanderthal and humans is briefly discussed however.

From what I can tell, what they did here was the following:

1. reconstructed a genome from their samples of Methanobrevibacter oralis subsp. neandertalensis.
2. compared the genomes to other Methanobrevibacter genomes including just one other M. oralis (this one from humans)
3. Inferred a possbile possible date range for the split between their M. oralis and that from humans 

It is cool and very interesting stuff.  See this figure for example.



And then based on this they write:

Date estimates using a strict molecular clock place the divergence between the M. oralis strains of Neanderthals and modern humans between 112–143 ka (95% highest posterior density interval; mean date of 126 ka) (Fig. 3b; see Supplementary Information). As this is long after the genomic divergence of Neanderthals and modern humans (450–750 ka)²⁹, it appears that commensal microbial species were transferred between the two hosts during subsequent interactions, potentially in the Near East³⁰.

So they are inferring transfer of commensal microbes based on molecular clock dating from one single M. oralis genome from Neanderthal and one from humans and a comparison of the inferred dating of their common ancestor versus the timing of supposed divergence between humans and Neanderthal. Personally it seems like a big big stretch to make that inference here. What if the dating from their analysis is off (such dating estimates are generally highly debated and unclear how accurate they are)?

But let's just say that this is in fact good evidence for some sort of more recent common ancestry of the M. oralis found in their sample and the M. oralis found in a human than one would expect based on knowledge of Neanderthal and human common ancestry. Does that mean swapping of the microbes between humans and Neanderthal? Not at all. Maybe the M. oralis comes from food. And if it is living in some sort of food source (could be animal, or plant or something else) and it comes into both humans and Neanderthal separately, then one could easily have a way for the one found in their Neanderthal sample to have a more recent common ancestry with the one found from humans than the common ancestry of the "hosts" here.

Interestingly, the genome they used to compare to Methanobrevibacter oralis JMR01 actually came from a fecal sample and not an oral sample - see Draft Genome Sequencing of Methanobrevibacter oralis Strain JMR01, Isolated from the Human Intestinal Microbiota. So this microbe is not solely found in the mouth and it apparently can survive transit between the mouth and another orifice, and may even be a gut resident (i.e., not just transiting).

So anyway - it seems woefully premature to conclude that the data they have here provides evidence for exchange between humans and Neanderthals of M. oralis. Could have occurred. But also could be separate colonization from similarly environmental sources.

And finally, even if we assume that the M. oralis was exchanged, which again there seems to be no good evidence for, what is to suggest that this was do due to kissing? Nothing as far as I can tell. How about sharing utensils? How about contact with fecal contaminated water (since M. oralis seems to do OK in feces)? Or I guess would could go extreme and say this could be evidence for oral anal contact between Neanderthal and humans, if we wanted to sensationalize this even more. After all, we do know many cases of microbes getting exchanged by oral - anal contact. But we don't do we? How about we stick to what we have good evidence for and then carefully discuss possibilities, of which kissing is one, but it is just one of many and it relies upon a lot of conclusions for which the evidence is tenuous at best.


This There is really amazing science in this work. But the kissing claims are premature as far as I can tell (I honestly hope I am wrong and that there is more data than presented in the paper, but if there is it should be presented somewhere - or maybe I have misinterpreted the paper - but I don't think so). If the claims are as premature as they seem to be, this is damaging in my mind to the field of microbiome science.
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UPDATE 3/10/17

Thanks to Ed Yong for updating his Atlantic article on this story to add a reference to my concerns.

He wrote

But after the paper was published, and several publications noted Weyrich’s suggestion about kissing in their headlines, Jonathan Eisen from the University of California, Davis, expressed skepticism about the claim. “Maybe the M. oralis comes from food,” he wrote in a blog post. It could have been picked up independently from the environment, or from water contaminated with feces, or from other kinds of sexual contact. A kissing route “it is just one of many and it relies upon a lot of conclusions for which the evidence is tenuous at best,” Eisen said.

UPDATE 2 - Made a Storify of some responses

Blast form the past - videos from 2002 research cruise at the Galapagos Rift

OK it is only 15 years after the fact but am posting some videos from the  2002 Galapagos Rift Expedition I went on May 24 - June 4, 2002.  It was the cruise honoring the 25th Anniversary of the discovery of deep sea hydrothermal vent ecosystems.



For more information see the web site from Dive and Discover

• Mission & Objectives
• Daily Updates
• Mail Buoy
• Scientists & Crew
• Interviews
• Hot Topics
• Slideshows
• Videos

Here is a playlist with all my videos, some from the cruise and some from the Galapagos Islands where the cruise started / stopped.  I have not edited any of the videos - just digitized everything from the tapes and posted them.  Apologies if anything is, well, inappropriate for any reason.

Useful post: How to read and understand a scientific paper: a guide for non-scientists

Just a quick one here.  This is a useful post for anyone interested in science literacy.  By Jennifer Raff: How to read and understand a scientific paper: a guide for non-scientists

These are actual living microbiologists #actuallivingscientist

Crossposting this - which I already posted at microBEnet I have been tracking #actuallivingscientist postings on Twitter compiled those by people doing microbiology. Actual living microbiologists.

The #falcons may have lost, but the birders won Twitter with #Superb_Owls vs. #Superbowl

Was fun yesterday watching all the punny posts about #Superb_Owls. I really love owls. I posted some too and also made a Storify of some of the posts of the day. Here are mine:

Real time blood glucose levels on Apple Watch

Made a storify of a discussion from Twitter. Loving my new Apple Watch with real time glucose values via my Dexcom CGM.

What to do with old Knome exome data ...

A little discussion from Twitter More coming but thought I would post this

A gloomy day at the #UCDavis Genome Center Halloween Symposium - a model for a #manel #yammm

It is a gloomy day, at least for me, at #UCDavis today.

Yes it is raining and cloudy.  But that is not the gloomy part. I like rain and clouds and we don't get enough of either around here. The issue for me is the Symposium happening today in my building.  Run by the UC Davis Genome Center, which I am a part of.  What is the problem?

Well here is the flier





That is nine presenters.  Eight of which are men. 

• S. Dinesh-Kumar
• Brett Phinney
• Anthony Herren
• Jessica Franco
• Jack Cuniff
• John Yates
• John Muchena
• Ilias Tagkopoulos
• Nuno Bandeira

That comes to 11% female speakers.  Not a good ratio.  But you know this is just one sample right?  It could be a random anomaly, or something else.

So - lets look at last years Halloween symposium.



That is five speakers, all men.

• Mingcheng Luo UC Davis
• Chris Streck 10X
• Marco Blanchette Dovetail
• Matthew Seetin PacBio
• Matthew Settles, UC Davis

OK so let's give it one more chance.  How about 2014.  See http://genomecenter.ucdavis.edu/2014/10/23/details-available-for-the-genome-center-halloween-symposium/

Four speakers. All male.

2014

• Bruce Draper UC Davis, Molecular and Cellular Biology
• Bruce Conklin, Gladstone Institute of Cardiovascular Disease, UCSF
• David Segal, UC Davis, Genome Center
• Dana Carroll, University of Utah, Department of Biochemistry

So over the last three years we have 94% male presenters. It is a better if you go back further. 2013 was 50-50.  2012 was  ~ 70-% male.  2011 was  55:45 or so.  But over the last three years something has devolved.  And no, I will not be attending.  And yes, I have made comments about this, but maybe too few.  

It is so frustrating to keep seeing this happening over and over in academia and science.  And to see it so close to home, well, it is really extraordinarily disappointing. 

I sent the organizers which I think has some great examples of how to run a diverse meeting.

Below are some articles worth looking at on the topic. 

• Diversity matters in planning journalism conferences by Steve Buttry
• show me the policy | cubist crystal by Jenny Martin
• Stop Agreeing To Be On All-Male Panels — Just Stop - Emily Peck the Huff Post.
• Increasing Diversity at Your Conference
• Promoting Gender Diversity at Conferences
• Encourage speaker diversity at synthetic biology conferences from Synberc 
• 6 Steps for Planning a Diverse Conference by Jessica Fleuti 
• White male lineup at medical meeting sparks 'public shaming' in STAT
• STEM Women: How Men Can Help, with Professor Jonathan Eisen ...
• Discussion of speaker diversity triggered by a #manel (Storify)
• Speaker gender balance at Society for the Neurobiology of Language conferences 2009–2015
• Countering gender bias at conferences Carrie Arnold in Science
• Ten Simple Rules to Achieve Conference Speaker Gender Balance by Jenny Martin 
• How to Add More Women Speakers to Your Meetings by Michelle Russell in PCMA Convene
• Welcoming Women at STEM Conferences – and Beyond - the StoryExchange 
• To Get More Female Conference Speakers - GenomeWeb
• Female Scientists Turn to Data to Fight Lack of Representation on Panels NY Times
• How likely is an all-male speakers list, statistically speaking? A mathematician weighs in.

I certainly feel partially responsible for this, because it is in my building and run by my Center.   Now I had nothing to do with this even, but still ...  I will do my best to make sure this does not happen ever again at the UC Davis Genome Center.  But I will not be attending this year's meeting.  

Thanks to all for "Suggestions for 11 year old daughter who wants to learn to code"

I am so thankful to the whole community out there who gave answers to my request for suggestions for my 11 year old daughter who wants to learn to code.

Today we were both home sick and when she said she was bored she then asked if we could try some of the examples people suggested.  And we ended up playing around with Python at Codeacademy and she spent hours on it.  So much fun. See below:

Daughter & I both home sick - she is bored - so we reviewed this https://t.co/T0F15Bv8MH & today she is learning Python via @Codecademy

— Jonathan Eisen (@phylogenomics) October 17, 2016

No - #FFS - no - I will not speak at your meeting given the lack of diversity of speakers

So a few days ago I got asked to do a paid speaking engagement for a meeting

Dear Dr. Eisen,

I hope this email finds you well!

We have a client that's interested in you speaking at their Autoimmune Conference in New York on March 24, 2017. 

Do you have a standard speaking fee/range that I can report back to my client?  If you're able to confirm your availability as well, that would be great!

The audience would be primarily physicians. 

Your consideration is very much appreciated!

Sincerely,

Sounded nice - getting paid to go to New York.  What could go wrong right?. Then I did some Googling to find out about the meeting.  Found it - the Interdisciplinary Autoimmune Summit: http://joinias.com. And, as I do for all meeting invites these days, I looked at their speaker line up.  For this years and previous years.  And well, I was not impressed.

A lot of men.  Men men men and men. So I wrote back

Matt Hahn @3rdreviewer talk at #UCDavis - pen and paper notes

Matt Hahn was at UC Davis giving a talk yesterday.

Yes @3rdreviewer has arrived at #UCDavis #holobiont #epigenetics #aquarius pic.twitter.com/yirR4rWdio

— Jonathan Eisen (@phylogenomics) October 6, 2016

I did not have my laptop available so took notes with - gasp - a pen and paper.  I thought it was quite a nice talk so am posting my notes here.  More about Matt and his work can be found here: http://www.indiana.edu/~hahnlab/.

The White Men's Microbiome Congress #YAMMM #Manel #Boycott

So I got this email this morning inviting me to attend a conference: the Second Annual Human Microbiome Congress in San Diego. (also called the North American Microbiome Congress).



And it struck me that all the featured speakers were men.




 Great.  So I decided to give them the benefit of the doubt, hoping that maybe if I looked at the rest of the speakers it would be better.

So I had to register on some web site to download the full agenda for the meeting.  And there were the featured speakers, rippling with diversity



So then I went to scroll through the document looking for the other speakers.

OMFG - what a joke.

Yet another biased meeting from Oxford Global - their meetings should be shunned #YAMMM #GenderBias

Well, Oxford Global has done it again.  They have found a way to be one of the most extremely gender biased conferences around.  Their 2016 Genome Editing Congress Speakers. Their web site lists 20 speakers, 19 of which are men.  (One of the men is listed twice - I am not sure if that is due to giving two talks or a mistake.  So this may be 19 speakers~ 95, 18 of which are men).  Regardless that comes to ~ 95% male speakers.

• Andre Choulika, CEO Cellectis
• Guna Rajagopal, VP – Global Head, Computational Sciences, Discovery Sciences Janssen
• Lorenz Mayr, VP & Global Head, Reagents & Assay Development Astrazeneca
• Zheng-Yi Chen, Associate Professor Harvard Medical School
• Daniel Anderson, Associate Professor MIT
• Marcello Maresca, Associate Principal Scientist Astrazeneca
• John Doench, Director; Associate Director, Genetic Perturbation Platform Broad Institute
• Chad Cowan, Associate Professor  Harvard
• Pablo Perez Pinera, Associate Professor University of Illinois
• Jim Collins, Professor MIT
• Channabasavaiah Gurumurthy, Director, Transgenic Core Facility University of Nebraska Medical School
• Danilo Maddalo, Senior Scientist and Lab Head Novartis Institutes for BioMedical Research
• Rodolphe Barrangou, Associate Professor North Carolina State University
• Stephanie Mohr, DRSC Director Harvard Medical School
• Robert Howes, Associate Director MedImmune
• Channabasavaiah Gurumurthy, Director, Transgenic Core Facility University of Nebraska Medical Center
• James Carothers, Assistant Professor University of Washington
• William Theodorus Hendriks, Instructor in Neurology Harvard Medical School
• Mark Osborn, Assistant Professor University of Minnesota
• Jeff Chamberlain, Professor University of Washington

1 and 19 were counted at Genome Editing USA Congress #OxfordGlobal. Learn more at GenderAvenger Tally

Sponsors of the meeting should be contacted about this:

Sadly this is a consistent pattern for Oxford Global. See for example Oxford Global Sequencing Meetings: Where MEN Tell You About Sequencing #YAMMM and also Time to boycott Oxford Global meetings due to blatant sexism

Really - we need as a community to stand up to these types of meetings.  Oxford Global meetings should be boycotted.  And the companies that sponsor their meetings are complicit in their gender bias.



---------------------------------------------
UPDATE  10/2 12:56 PM - decided to look at another one of their meetings that is linked from this one

2nd Annual Next Generation Sequencing USA Congress
3-4 October 2016, Boston, USA

83 % male speakers.  Grand.

• James Knight, Director of Bioinformatics Yale University
• John Quackenbush, Professor Dana-Farber Cancer Institute
• Shanrong Zhao, Director Pfizer Inc.
• Nazneen Aziz, Research Professor Arizona State University
• George Weinstock, Director and Professor Jackson Laboratory for Genomic Medicine
• Alexander Wait Zaranek, Director Informatics Harvard Medical School
• Rong Mao, Medical Director, Molecular Genetics and Genomics, ARUP Laboratories; Associate Professor, Pathology University of Utah School of Medicine
• Mark Gerstein, Albert L Williams Professor of Biomedical Informatics, Molecular Biophysics & Biochemistry, and Computer Science Co-Director of the Yale Program in Computational Biology & Bioinformatics
• James Willey, Professor of Medicine and Pathology University of Toledo
• Neil R. Smalheiser, Associate Professor in Psychiatry University of Illinois College of Medicine
• Mark Borodovsky, Regents’ Professor Georgia Tech
• Scott J. Tebbutt, Associate Professor & Chief Scientific Officer University of British Columbia & PROOF Centre of Excellence
• Michael Fraser, Program Director, Cancer Genomics, Radiation Medicine Program Princess Margaret Cancer Centre
• Justin Johnson, Associate Director and Principal Scientist AstraZeneca
• Leonora Balaj, Instructor in Neurology Massachusetts General Hospital Harvard Medical School
• Aleksandra Markovets, Senior Scientist AstraZeneca
• Baohong Zhang, Director of Clinical Bioinformatics Pfizer, Inc.
• Steven Hart, Assistant Professor of Biomedical Informatics Mayo Clinic
• Manolis Kellis, Professor and Head, MIT Computational Biology Group MIT
• John Methot, Head of Scientific Computing Biogen
• Andrew Hollinger, Associate Director: Scientific Communications Broad Institute
• Yingtao Bi, Senior Manager in Statistics Abbvie Bioresearch Center
• Paul Blainey, Assistant Professor of Biological Engineering, MIT and Core Faculty Member Broad Institute of MIT & Harvard

4 and 19 were counted at #oxfordglobal. Learn more at GenderAvenger Tally

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For other posts on STEM Diversity see here.

Wrap up from Gender Bias Under the Microscope Symposium #RFUSymposium #GenderBias

Had an amazing time at Rosalind Franklin University for their Gender Bias Under the Microscope Symposium. I made a Storify about it here:

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For other posts on STEM Diversity see here.

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Storify of talk by @CameronNeylon at #UCDavis on "Excellence is Bullshit"

Made a Storify

No thanks Precision Medicine #PMWC2017 - I don't want to go to your $&*@(#@( #manel #yammm #biased meeting

Today I got this email, ostensibly from Keith Yamamoto, who I have interacted with a bit over the years, including in the writing of the NAS "New Biology" report.



So I decided to check out the meeting site.  Precision Medicine World Conference. Hosted by Stanford and UCSF and Duke and Others.  And also a "manel". Also known as a YAMMM (yet another mostly male meeting).  A festival in fact of men.  So so so many men listed as speakers. Here is my round up.




Just so sick of meetings like this.  Apparently Keith Yamamoto and UCSF and Duke and Stanford and all the Sponsors endorse having a meeting where about 1 in 6 of the speakers are women.  No thanks. Not interested.  I am sure they can all make a litany of excuses.  But I am so tired of hearing them.  In the end the only way to get some of these groups to change their practices is to boycott their meetings.  And to publicly discuss, with the sponsors and speakers and organizers, why their meeting is not OK.


UPDATE 1 - Some responses and discussion on Twitter

UC Davis Coffee Course covered by NPR

A mini rant about diversity at meetings #STEMDiversity #YAMMM #manel

Congratulations SynbioBeta #SBBSF16 - you are having a #YAMMMy #manel

Well this is disappointing.

Someone sent me an announcement for SynBioBeta SF 2016 - SynBioBeta possibly thinking I would go to it.  Since it was local I decided to check it out.  And, well, the 1st thing I did was to look at the gender balance of the speakers (as much as I could infer from a quick skim).  And it did not look good.  So I dug into it in more detail.

They have a speaker page and I went through most of them to make sure my inference of gender was correct (based on looking at the pronouns used to describe them in their speaker bio and also in other web sites).  I know this is imperfect but seems potentially a decent estimator.  And low an behold when you sum it all up you get 79% male speakers vs. 21% female speakers.  They could definitely do better.

Viruses viruses viruses viruses viruses viruses viruses.

Actually, the title is clearly insufficient. [Viruses]^100 or something like that would be better.

And here is a story by Michaeleen Doucleff from NPR about viruses in the human microbiome with some quotes from me.