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

Ugg

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.