Wednesday, August 09, 2017

The Massry Prize is a #YAMMA (yet another mostly male award) #MatildaEffect #Massry #GenderBias

I was really pleased to see the announcement that the 2017 Massry Prize was awarded to Norm Pace, Jeffrey Gordon and Rob Knight.  Alas, then someone pointed me to the web site listing past winners of the prize. Massry Prize.  And I compiled the list (with some help from Wikipedia)

Massry Prize
Yet Another Mostly Male Award
  1. 1996 Michael Berridge 
  2. 1997 Judah Folkman 
  3. 1998 Mark Ptashne 
  4. 1999 Gunter Blobel 
  5. 2000 Leland H. Hartwell 
  6. 2001 Avram Hershko
  7. 2001 Alexander Varshavsky 
  8. 2002 Mario Capecchi
  9. 2002 Oliver Smithies 
  10. 2003 Roger Kornberg
  11. 2003 David Allis 
  12. 2003 Michael Grunstein 
  13. 2004 Ada Yonath 
  14. 2004 Harry Noller 
  15. 2005 Andrew Fire
  16. 2004 Craig Mello 
  17. 2004 David Baulcombe 
  18. 2006 Akira Endo
  19. 2007 Michael Phelps 
  20. 2008 Shinya Yamanaka
  21. 2008 James A. Thomson
  22. 2008 Rudolf Jaenisch 
  23. 2009 Gary Ruvkun
  24. 2009 Victor Ambros 
  25. 2010 Randy Schekman 
  26. 2011 F. Ulrich Hartl 
  27. 2011 Arthur Horwich
  28. 2012 Michael Rosbash
  29. 2012 Jeffrey C. Hall
  30. 2012 Michael W. Young 
  31. 2013 Michael Sheetz
  32. 2013 James A. Spudich 
  33. 2013 Ronald D. Vale 
  34. 2014 Steven Rosenberg
  35. 2014 Zelig Eshhar 
  36. 2014 James P. Allison
  37. 2015 Philippe Horvath
  38. 2015 Jennifer Doudna 
  39. 2015 Emmanuelle Charpentier
  40. 2016 Gero Miesenböck
  41. 2016 Peter Hegemann
  42. 2016 Karl Deisseroth
  43. 2017 Rob Knight
  44. 2017 Jeff Gordon
  45. 2017 Norm Pace
42 male
3 female

I colored them based on my inference of gender. I realize that I may have some of this wrong and that using a binary system is not right in many cases but I think this certainly shows a pattern.  I also realize there are many possible explanations for the imbalance here but I think it is reasonable to consider that bias against women may be a component of this. 

Some useful reading in regard to prizes in the sciences:
Not sure what to do here with this information.  I deeply respect the award winners here and think they are highly deserving of important science awards.  But it pains me to see such a big skew in the gender balance of winners of this Massry Prize and think, sadly, that there is likely some kind of bias at work here.  When there is a bias against recognizing the achievements of women it is known as the Matilda Effect.  I suggest everyone involved in handing out awards such as this, and anyone reporting on such awards, should read up on it.

I note - I posted the gender ratio of winners of this award to the Gender Avenger site. See below:

Thursday, August 03, 2017

#SciFoo 2017 here I come

Well, I am going back to SciFoo. This is a meeting that happens at Google, is organized by O'Reilly Media and Nature and Google and Digital Science and others.  I went in 2012, 2007 and 2006.  And every single time it was life altering.  I will try to post while there but it can be distracting ...Here are some notes and posts from the past scifoos I have attended.


Storify I made:

Monday, July 24, 2017

Another white men's microbiome meeting from Kisaco #YAMMM #manel #STEMDiversity

Well, this is really unpleasant.

Last year I blogged about a what I called "The White Men's Microbiome Congress." The gender balance of the meeting was so bad I called for a boycott. And my call seemed to have some impact as many people refused to participate and then the meeting organizers from Kisaco Research responded, apologized for the gender bias, and made some attempts to at least try to fix things. For example they posted on my blog:
We recognize that it is our responsibility to help ensure that the speaker faculty reflect the diversity and culture of the field and science as a whole. In this instance we failed to live up to our own standards of sensitivity and diversity, for which we sincerely apologize. Kisaco Research is deeply committed to producing events that represent the diversity of the scientific fields we work with. We are embarrassed that this has been previously overlooked and are currently working to make this, and all other programmes, ones that the top scientists are proud to be a part of. 
And they did seem to try to make the meeting I critiqued less biased.

And thus it was really disturbing to me when someone sent me the invite they received to a microbiome meeting organized by this group and pointed out that it had the same issue. I went to the web site for this new meeting - the "3rd annual European microbiome congress (see The Microbiome Congress – Europe – Kisaco Research). And it confirmed my fears.

95% of the highlighted speakers are male (as always, I note, assessing the gender balance of a meeting is not always straight forward.  In this case I looked at the web sites of the speakers and other descriptions of them to see what pronouns were used to describe them.  I think my assessment is accurate but I apologize if I made mistakes). And all of them appear to be white.  It is a meeting for white men to speak at.  The field of microbiome studies is rich and diverse in many ways - including in the scientists and others who work on the topic.  It would not have been hard to come up with a more diverse set of speakers.  In fact, the field is so diverse in terms of researchers that I think this speaker line up - especially in light of the previous meeting - is evidence for bias.   I am not sure where that bias comes in (it could be at invitations, at acceptances, or other places) but it is pretty clear this is not a random selection of top microbiome researchers.

As this is a pattern from Kisaco Research I am calling for the following
  • People should boycott this meeting. That is, do not attend this meeting.
  • People should Boycott all Kisaco meetings. This is a pattern for Kisaco, and not a good one.  Nobody should attend any of their meetings
  • The meeting sponsors should withdraw support for this meeting. The listed sponsors include Synthetic BiologicQiagenProDigestAffymetrix and Zymo Research. I encourage people to contact them about this and pressure them to rescind their sponsorship.  I have already contacted Zymo, for which I am an advisor.  I will let people know how they respond. 
  • The speakers should cancel their participation.  A meeting cannot go on without the speakers. The listed speakers include:
Of course, it would be better to prevent such things from happening in the future.  Some things to consider that will start to shift away from meetings with poor diversity of presenters:
  • Make diversity of presenters one of the factors you consider when deciding whether or not to accept invitations to speak at or attend a meeting. Some ways to make an informed decision here include
    • looking at past meetings by the same organizers
    • asking for a list of presenters for the meeting one is invited to
    • asking if the meeting has any policies on diversity
  • When you are involved in organizing a meeting work to make it a stellar meeting that also happens to have a diverse collection of presenters (diverse in background,  race and ethnicity, kills, perspectives, gender, types of institutions, careers stages, country of origin, and more). 
  • Develop diversity policies for meetings in which you are involved
  • If you are on the sponsorship side of things - require meeting organizers to have a diversity policy and to show their prior track records before you offer support
  • Develop and support practices and policies that would help make meetings more diverse 

Also check out some of these articles and posts

It is entirely possible to run meetings where there is no bias against particular groups in the presenter line up.  It is also possible to embrace diversity and all of its benefits and make a meeting that is simply better than a meeting where diversity is not embraced.  It does take some effort.  But it is worth it.

UPDATE. Making a Storify of some responses

Saturday, July 22, 2017

Today in misleading, dangerous, overselling of the microbiome - UNC on babies and cognitive development

Uggh. Was pointed to this on Twitter:

In baby's dirty diapers, the clues to baby's brain development | EurekAlert! Science News

And I read the PR and made a quick Twitter response but decided to fill that in here a bit.
Basically the study being discussed found a correlation between the microbiome in babies poop and their cognitive development. There are 100s of possible causes for such a correlation. But the press release misleading went on about how their work suggests they maybe able to somehow intervene to guide development by manipulating the microbiome. Ridiculous.

Here are some problematic quotes

  • "In baby's dirty diapers, the clues to baby's brain development"
    • Not really any clues providing in this work towards brain development. They have an interesting observation. It is unclear if it provides any insight into brain development.
  • Findings from the UNC School of Medicine shed light on the surprising role of bacteria in how our brains develop during the first years of life
    • No no no no no and no. They do not show ANY role of bacteria in how brains develop.
  • Our work suggests that an 'optimal' microbiome for cognitive and psychiatric outcomes may be different than an 'optimal' microbiome for other outcomes."
    • Oh #FFS. They do not show in any way what is or is not an "optimal" micro biome. They have a $*(#($# correlation. That is it.
  • Though the findings are preliminary, they suggest that early intervention may hold the key to optimizing cognitive development.
    • Well sure if you use the term "may" generously here they may hold such a key. But if you want to use it generously then these results may also suggest that UNC may be a dangerous place to bring babies because some of them may get a defective microbiome there which may lead them to have cognitive problems. You see, the findings in this work actually do not really suggest anything about early intervention at this point. Ridiculous to even suggest it.
  • One was that when measuring the microbiome at age one, we already see the emergence of adult-like gut microbiome communities -- which means that the ideal time for intervention would be before age 1."
    • No not really. Even if intervention was actually indicated here (which again, it is not) this does not mean that the time to intervene can be determined by looking at where they get an "adult" like micro biome. Because they have no mechanism here. It could be something in the baby and adult microbiome that is doing this (again, assuming there is a causal connection which there is not one shred of evidence for).

And then this is the worst.
"Big picture: these results suggest you may be able to guide the development of the microbiome to optimize cognitive development or reduce the risk for disorders like autism which can include problems with cognition and language," said Knickmeyer. "How you guide that development is an open question because we have to understand what the individual's microbiome is and how to shift it. And this is something the scientific community is just beginning to work on."
What the living #$*@(#(@? Now they are suggesting that their results say you may be able to optimize cognitive development and reduce the risk of autism. All from a simple correlation for which they have no clue whether there is any mechanistic connection. Offensive. Dangerous. Ridiculous. Sad.

Tuesday, July 04, 2017

Human microbiome studies really are oversold, new study suggests #UCLA #Microbiomania

Blargh.  I saw this headline and I was suckered in.  I thought there might actually be something novel behind it:: Human emotions really are affected by gut bacteria, new study suggests - ScienceAlert But no - despite the headline, this is just about a paper that showed correlation between microbiome community patterns and various behavioral traits. Not a shred of cause vs effect tested.  And yet despite that this is just a correlative study, the article just completely overstates the implications
"But it's clear that there's something going on between the organisms in our gut and the thoughts and feelings we experience, and the sooner we delve into this, the sooner we'll comprehend just how emotionally powerful our 'second brain' really is."
No no no no no and no.  They do not show ANY connection between our thoughts and our microbiome.  They just report a correlation.  It could be that people with different thought patterns eat differently.  Or people with different thought patterns exercise differently.  Or $(#($(#@@ just abo9ut anything. Alas, many other stories about this work also make false inferences. See the Huffington Post for example: Your Gut Bacteria Really Do Affect Your Emotions 
"A new study looked at how ‘microbiota’ bacteria in the human gut influences our emotional responses, as the evidence suggests there is a direct correlation between the two."
 Again, no no no no and no.  They do not study how microbiota influence emotional responses.

And how about the Daily Mail: Gut feelings are real: Some people have stomach bacteria that makes them more anxious and stressed, study shows. What a horribly misleading, inaccurate headline.

So one might ask - where could these news sources have gotten the idea that this was more than a correlative study?  Hmm.  I wonder.  Maybe we should look for any press releases from UCLA?  So I googled the lead authors name and found this:

Research suggests association between gut bacteria and emotion published on June 29 from UCLA.  And this PR does not start well.  The first sentence is simply wrong at best.  Misleading and deceptive I think:
Researchers have identified gut microbiota that interact with brain regions associated with mood and behavior.
No no no no no and no.  There is no evidence that these gut microbiota interact with brain regions in any way.  Later in the article there is a bit of a caveat -
Researchers do not yet know whether bacteria in the gut influence the development of the brain and its activity when unpleasant emotional content is encountered, or if existing differences in the brain influence the type of bacteria that reside in the gut.
But it is too little too late.  And it is not actually accurate either.  There are other possibilities - like there is a third factor that affects both the microbiome and the brain but where the brain and microbiome don't impact each other.  What could that factor be? Oh I don't know - how about something called the immune system?  It is just bad science to report that this has to be the gut affecting the brain or the brain affecting the gut.

And for this I am giving out a coveted "Overselling the Microbiome Award" to UCLA and their Press Office.

I have also rewritten the original headline that caught my attention.

There.  I feel better already.  Must be my microbiome.

Monday, July 03, 2017

A time capsule from my father's youth - the secrets of a 62 year old Bar Mitzvah book on his 75th birthday

Today, July 3, 2017, is my father - Howard Jay Eisen's birthday.  He would have been 75 today.  I am sure we would have had a grand celebration of some kind.  I will make a toast in his honor tonight.

Sadly, he is no longer alive.  He passed away in 1987, when I was a freshman in college.  It was a painful ending of his life.  I have written about this.  As has my brother Michael.  As have some other people here and there. If you want to know more about that, well, here are some links to read.

But that is not what I want to write about today.  The pain of his suicide will be with me forever I am sure.  But I want to focus on his life.  And that I know remarkably little about.  So it was with great interest that a few years ago his sister Arleen came to visit us in California.  And as part of this visit she gave me my father's Bar Mitzvah Book.  

I glanced at it and then it sat in a box for a while.  I have never been religious and did not have a Bar Mitzvah myself.  So it seemed foreign to me.  

But then, when Arleen passed away relatively suddenly, I felt really disconnected form my father's history.  And so one day I opened the book and leafed through it more carefully. And I became a bit obsessed with it.  The book had dozens of pictures from the event.  And cards and telegrams congratulating my father.  And all sorts of notes and notations of various kinds.  I barely recognized any of the people.  Of course, this was from 1955 so that is not that surprising.  But part of this is that I have never been that close to my father's family.  I always got along with them, but just never saw them that often before my father died and even less afterwards.  So the key to me was - how could I figure out just what was in the book. And more importantly to me, could I figure out who was at this event.  This was one of the only tangible things I had to hold about my father's childhood.  I did not know too many stories.  I did not have many artifacts of any kind.  And here was this major major event.  And I literally had the book about it.  

So today I am here to tell you, I have digs into this book.  And stunningly, it not only told me about one event, it told me about my family.  A lot.  It did this because I was able to figure out who most of the people were at the Bar Mitzvah - and most of them were family.  In addition, I have used some family tree databases such as Ancestry and My Heritage to track down information about these people and have been able to use this one book to basically figure out, I think quite accurately, many generations of my father's family tree.

Friday, June 30, 2017

Thank you Gizmodo and Ryan Mandelbaum for anti-poop-doping story

Thank you Gizmodo and Ryan F. Mandelbaum for this: Athlete Poop Won't Improve Your Athletic Performance.  I like this in particular
“A bunch of elite cyclists have a microbiome that looks like this,” the way Petersen describes, fecal transplant expert and professor Elizabeth Hohmann from Massachusetts General Hospital told Gizmodo. “So what? Is that because of the foods they eat?” After all, it could be the lifestyle that makes their microbiome look the way it does, not the microbiome that makes them better performers. “There are associations, but not causal. The idea that [microorganisms like] Methanobrevibacter smithii or Prevotella will make you a better performer is ridiculous.”
and this
And the fact that Petersen felt better after a fecal transplant is an anecdote that could simply be the placebo effect in action.

and this
There’s always the chance that poop doping could be harmful, too. “There’s the risk of transmission of infections agents for sure,”
and more definitely worth a read.

Wednesday, June 28, 2017

More awful reporting on the "poop doping" claimed by Dr. Lauren Peterson


Been trying to stamp out the awful reporting on the poop doping claims of Dr. Lauren Peterson.  See

But the crap keeps flowing.  Here is the last - in the NY Post: Poop transplants are the final frontier in athletic doping | New York Post

Here are some quotes from the story and my comments about them.

  • "The treatment helped her battle Lyme Disease, however, there was a downside."
    • No evidence exists that this treatment helped her battle 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,”"
    • This is reported with no caveats when there should be plenty.  This is almost certainly a incorrect interpretation by her.
  • "What’s worse, during graduate school Petersen had her digestive system tested and discovered that she was full of gram-negative pathogens. Common strains of the pathogens include E.coli and Salmonella."
    • Almost certainly this is also a misinterpretation.  Most tests such as those by American Gut which she claimed to have done would not have been able to say if she had pathogenic versions of these bugs.
  • The results were astounding
    • This implies cause and effect which has not been shown.
  • It turns out that Petersen probably would not have been doing as well if she’d gotten a couch potato’s poop. 
    • No evidence for this exists.
  • she already knows that it plays a critical part of muscle recovery.
    • I am deeply skeptical of this claim. 
  • Besides creating flatulence, decreasing the amount of hydrogen in our gut increases the amount of calories that are extracted from food, a study published in PLos One suggests.
    • It is really great that they link to a paper thus trying to show there is evidence for a claim.  Alas, the paper does not show what is claimed here.  This paper is just about comparing abundance of different microbes in obese, anorexic and control patients.  So to say they "suggest" that this papers shows this methanogen is involved in increasing the amount of calories extracted from food is misleading.  The authors hypothesize that sure.  So in one sense they "suggest" this but the way this is written implies they actually studied that, when they did not.

Sunday, June 25, 2017

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.

Wednesday, June 21, 2017

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

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.

UPDATE June 21 2:54 PM

Marissa Payne updated her story with some comments from me


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.”

Monday, June 12, 2017

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.

Thursday, May 25, 2017

Storify of Day 1 of "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.

Monday, May 01, 2017

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. 
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.

Thursday, March 09, 2017

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.

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

Wednesday, March 01, 2017

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

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.

Wednesday, February 08, 2017

Monday, February 06, 2017

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: