Tuesday, September 13, 2016

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

Saturday, September 03, 2016

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.














Tuesday, August 30, 2016

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.

Friday, July 22, 2016

Today's misleading overselling the #microbiome - U. Chicago on Alzheimer's and gut microbes


Well, this is disappointing if not disturbing

A new paper is out that has some interesting findings but the paper itself, and the press release form the authors (at University of Chicago) really goes overboard in misstating the findings.

Here is the paper in Scientific Reports. I purposefully am not putting the title of the paper here in the post yet, because amazingly, even the title is misleading.

But here is what a summary of what they showed, based on their results section, which seems interesting and sound
  • Antibiotic treatment of a variety of mice showed alterations in the GI microbiome and in various inflammatory markers circulating in the blood
  • Male mice treated with this antibiotic regime showed reduced Aβ plaque deposition but increased soluble Aβ levels
  • Reactive gliosis surrounding Aβ plaques is reduced in male mice treated with this antibiotic regime 
This is not all they report as they also discuss various controls and other observations about these mice and their brains and their responses to the antibiotic treatment.  

But what they do not report on is any evidence of anything other than a correlation between the GI microbiome changes and the inflammatory markers and the reduced Aβ plaque deposition.  They even state this VERY BRIEFLY in their paper
We are fully cognizant of the fact that the findings reported herein are purely correlative and do not elucidate precise mechanism(s). 
Yet then through other papers parts of the paper they misstate what they find and somehow, almost magically, turn this correlation into evidence for a causative connection.  For example in the abstract
These findings suggest the gut microbiota community diversity can regulate host innate immunity mechanisms that impact Aβ amyloidosis.
No. These findings are consistent with that.  They are also consistent with, for example, the antibiotics affecting microbes in the brain which in turn could affect inflammatory markers.  Or microbes on the skin.  Or in the blood.  Or elsewhere.  I don't see any evidence here for a causative connection between the gut microbes (which are certainly affected by these antibiotics) and the plaque.

Yet even worse is that this misrepresentation of a causative connection makes it into the title of the article
Antibiotic-induced perturbations in gut microbial diversity influences neuro-inflammation and amyloidosis in a murine model of Alzheimer’s disease


No no no no no no no no.  No evidence that the perturbations in the gut microbes are directly influencing anything in the brain.  It is a good model.  But they need to be more careful with their wording.

And sadly, this gets even worse in the press release about the paper: Antibiotics weaken Alzheimer's disease progression through changes in the gut microbiome | EurekAlert! Science News

What?  This "through changes in the gut microbiome" is just completely misrepresenting what was shown in the paper.

Here are some misleading parts of the PR
The study, published July 21, 2016, in Scientific Reports, also showed significant changes in the gut microbiome after antibiotic treatment, suggesting the composition and diversity of bacteria in the gut play an important role in regulating immune system activity that impacts progression of Alzheimer's disease.
Nope. Nope. and Nope.

Thankfully there are a few caveats in the PR too but that does not balance misleading statements.  The worst is saved for the end
"There's probably not going to be a cure for Alzheimer's disease for several generations, because we know there are changes occurring in the brain and central nervous system 15 to 20 years before clinical onset," he said. "We have to find ways to intervene when a patient starts showing clinical signs, and if we learn how changes in gut bacteria affect onset or progression, or how the molecules they produce interact with the nervous system, we could use that to create a new kind of personalized medicine."
Basically, saying there will be a cure for Alzheimer's. And then saying if we learn HOW (not if) gut microbes affect onset or progression, then we can better cure or treat this disease.  This is just too bold and misleading for my taste.  Nice paper.  Interesting work and implications. But it is misleading to say they have shown any causative connection between gut microbes and Alzheimer's in this paper and also very misleading to start to talk about how they will use this to lead to treatments or cures.

Oh, and did I mention this was in mice not humans?  So how do they get from a correlative study in mice to how gut microbes affect progression of Alzheimer's in humans?  Really this is not OK, even to hint at.

And of course, which such misleading material in their own paper and in their PR it is not surprising that some of the reporting on this is going awry.

See the Daily Express for example



And the Business Standard


And I am sure many more to come.  Scientists have to be more careful with discussing and presenting the implications of their work.  I love the microbiome field and the possible implications to me are enormous for the role of the microbiome in various areas of biology.  But misrepresenting ones findings, especially when it comes to human diseases, is dangerous and bad for science and bad for the microbiome field.  The author's of the paper and the people behind the PR at the University of Chicago should publish a correction of the PR and also publish a correction of their paper to correct the misleading representations. And for their misleading material in their paper and in the PR I am giving them a coveted "Overselling the Microbiome" award.



Thursday, July 14, 2016

Overselling the Microbiome Award for @nytimes on thumb sucking, nail biting protecting from allergy



I am continually torn about handing out "overselling the microbiome" awards to many "stories" that are coming out recently on new scientific studies.  On the one hand, many of these studies are quite interesting.  On the other hand, a huge number of them oversell the implications of the work.  And for some reason it seems to me that studies that could indicate a positive role for microbes in some way seem to end up with more misrepresentation than other types of work.  Mind you, I truly believe the cloud of microbes living in and on various plants and animals are likely to play fundamental roles in all sorts of important functions.  But my thinking this and my thinking it is likely does not mean we should go around overstating the implications of work in this area.

And that brings me to the latest example of such overselling  ... a story about thumb sucking and nail biting as covered in the New York Times: Thumb Suckers and Nail Biters May Develop Fewer Allergies

The science here is interesting  - it is based on a new paper testing for associations between thumb sucking and nail biting on the one hand and atopic sensitization, asthma and hay fever on the other.  The paper found the following: Children who suck their thumbs or bite their nails are less likely to have atopic sensitization in childhood and adulthood.

Interesting.  But a key part of this is that they discovered a correlation.  Lots and lots and lots of possible explanations for this correlation including some examined in the paper but none of which have been proven.  Some news reports do a good job of covering the topic and discussing how this is still just a correlative observation.  For example see this Washington Post article by Lateshia Beachum.  There they report on the authors comments where the authors seem to think this supports the hygiene hypothesis
“The findings support the ‘hygiene hypothesis,’ which suggests that being exposed to microbes as a child reduces your risk of developing allergies,” Hancox said in a statement.
But then immediately this is countered by some more careful thoughts
Hirsh Komarow, a staff clinician at the National Institute of Allergy and Infectious Diseases, isn’t entirely convinced about the study’s conclusions. “It’s an interesting observation, but it needs more analysis,” Komarow said.
And then he is further quoted with other possible explanations
Komarow also suggested that thumb-sucking and nail-biting could be indicative behaviors that either thwart or encourage allergic reactions. He said being part of a large family and being exposed to microbes from many siblings may affect a child’s allergic sensitization.
And there are other articles out there with a decent amount of caveating.  But sadly the New York Times article by Perri Klass is not so tempered. Here are some of what I consider to be statements without enough caveating or countering:
A new study suggests that those habits in children ages 5 to 11 may indeed increase exposure to microbes, but that that may not be all bad.
No no no.  The new study did not suggest that.  The new study is consistent with that, but it is consistent with many other explanations.

And then there is this:
These differences could not be explained by other factors that are associated with allergic risk. The researchers controlled for pets, parents with allergies, breast-feeding, socioeconomic status and more. But though the former thumb-suckers and nail-biters were less likely to show allergic sensitization, there was no significant difference in their likelihood of having asthma or hay fever.
Well it is nice that the authors of the paper tested for some other possible explanations.  But it is a giant and inappropriate leap to go from that to "These differences could not be explained by other factors that are associated with allergic risk"

And then there are multiple quotes from the authors which are not really caveated enough or at all
Robert J. Hancox, one of the authors of the study, is an associate professor in the Department of Preventive and Social Medicine at Dunedin School of Medicine, a department that is particularly oriented toward the study of diseases’ causes and risk factors. He said in an email, “The hygiene hypothesis is interesting because it suggests that lifestyle factors may be responsible for the rise in allergic diseases in recent decades. Obviously hygiene has very many benefits, but perhaps this is a downside. The hygiene hypothesis is still unproven and controversial, but this is another piece of evidence that it could be true.”
Some caveats here but not enough.  This is not "evidence that it could be true" but rather it is data consistent with that model, but also consistent with other models that have nothing to do with the hygiene hypothesis.

And then there is this:
Malcolm Sears, one of the authors of the paper, a professor of medicine at McMaster University in Hamilton, Ontario, who was the original leader for the asthma allergy component of the New Zealand study, said, “Early exposure in many areas is looking as if it’s more protective than hazardous, and I think we’ve just added one more interesting piece to that information.”
No this study did not show that early exposure from thumb sucking or nail biting has any protective benefit.  It showed a correlation between thumb sucking/nail biting and lower risk of sensitization.  It did not show any causal connection.  And even if a causal connection were found, one would still have to test for what was the mechanism and the mechanism could be many things unconnected to microbial exposure.

And then there is this
Dr. Hancox pointed out that the study does not show any mechanism to account for the association. “Even if we assume that the protective effect is due to exposure to microbial organisms, we don’t know which organisms are beneficial or how they actually influence immune function in this way.”

Yes, this is good in some ways.  But why would we assume this?  Stating this without caveats makes it seem like we should assume this.

and
Dr. Sears said, “My excitement is not so much that sucking your thumb is good as that it shows the power of a longitudinal study.” (A longitudinal study is one that gathers data from the same subjects repeatedly over a period of time.) And in fact, as researchers tease out the complex ramifications of childhood exposures, it’s intriguing to look at long-term associations between childhood behavior and adult immune function, by watching what happens over decades. 
None of these quotes are really caveating the claims.  And then the article ends with a statement that seems to indicate that this is all a proven fact
So perhaps the results of this study help us look at these habits with slightly different eyes, as pieces of a complicated lifelong relationship between children and the environments they sample as they grow, which shape their health and their physiology in lasting ways.
Yes, this study is interesting.  And yes, it might be indicative of a causative connection between exposure to microbes on thumbs and nails and reducing risk to allergy.  But no, the study did not show that there is a causative connection, just a correlation.  And thus we cannot conclude at this point that we should "look at these habits with slightly different eyes, as pieces of a complicated lifelong relationship between children and the environments."  The correlation could be due to other factors that have nothing to do with these habits.  And this is just a massive difference.  Shame on the New York Times for not reporting on this carefully enough.

And thus I am awarding a coveted Overselling the Microbiome Award to the New York Times and Perri Klass.

Hat tip to Mark Sagoff for pointing me to the NY Times article.






Sunday, July 10, 2016

Today in Overselling the #microbiome: Lick-hiker's guide to Inner Strength

Well, thanks, I think to Christie Aschwanden https://christieaschwanden.com for pointing me to this.

Valio unveils Lick-hiker’s Guide to Inner Strength with travel presenter Ian Wright - hasan & partners




Valio - Gefilus Trailer from hasan & partners on Vimeo.

From the Press Release
International travel presenter Ian Wright is on a mission to seek out and lick the dirtiest locations in Europe for The Lick-hiker’s Guide to Inner Strength, a campaign that promotes the virtues of Gefilus, a good bacteria product range by dairy giant, Valio.
Simultaneously almost certainly over-promoting the benefits of this one probiotic and also the risks of licking things all over the globe.
Our 25-minute documentary sees Wright’s tongue come into contact with places that harbour bad bacteria - all in the name of testing immunity, gut health, and science. These include a metro station, public toilet, telephone, kindergarten, river, €10 note, bronze statue and Tottenham Hotspur FC.
Did they really have to pick on Tottenham?
Valio commissioned hasan & partners to demonstrate the power of Gefilus, which contains the friendly Lactobacillus rhamnosus GG and vitamins. Lactobacillus rhamnosus GG is the world’s most researched lactic acid bacterium and its qualities have since been scrutinized in more than 800 scientific studies globally.
Umm - just because there are 800 papers does not mean it is necessarily good for you. I mean, published papers is a good thing. But there are also 1000s of papers on anthrax and smallpox ...
Armed with bottles of good bacteria and a luminometer to count germs, the two-week tongue tour of Europe tests Wright’s taste buds and nerve to the limit. Viewers will find out if he survived the ordeal without contracting any stomach bugs and where in the world is the location with the worst bacterial score.
OK - well then. A luminometer will reveal everything you need to know about a sample of microbes. We should just use them for every microbial study everywhere (nothing against luminometers per se, but they really are not what is needed here).
Jussi Lindholm, COO of hasan & partners, comments: "Good bacteria in Gefilus products has been carefully studied and people believe in it. But seeing is believing, so the documentary is both educational and fun, designed to physically draw attention to the link between the gut, our inner strength, and our wellbeing. World traveller Ian Wright has experienced many challenges and Gefilus was probably the weirdest."
OK. Doesn't actually seem that weird. Just oversold ...

Here is the full documentary