Wednesday, October 07, 2015

Wrap up of talk by Rich Lenski at UC Davis

Rich Lenski gave a talk today at UC Davis - part of a two talk series. This was a presentation more for the public and tomorrow he gives one more for the science crowd. Today's talk was a really nice overview of Lenski's work on long term evolution experiments in E. coli. I made a Storify of the tweets about the talk:

Monday, September 28, 2015

Journal Club at #UCDavis on Co-evolution of Microbiomes and Hosts - ideas wanted

I am going to be running a journal club this quarter at UC Davis for the Population Biology Graduate Group.  The topic is Co-evoution of Microbiomes and Hosts.

Meeting time is 12:10-1:00 PM if you want to participate let me know.

A link to the Draft Outline is here. And I am trying to embed it in this post ...

If anyone has other ideas for interesting papers on co-evolution of microbiomes and hosts, please let me know and I will add them to the list. Stay tuned as each week I will post about the discussion topics and notes from the discussions.

Saturday, September 12, 2015

Roundup of microBEnet posts of (possible) interest

I spend a decent amount of my blogging time these days writing posts for microBEnet (the microbiology of the built environment network) which is part of a project funded in my lab by the Sloan Foundation.

Some recent posts that may be of interest are listed below:

Tuesday, September 08, 2015

Today's awful overselling of the microbiome - Robynne Chutkan on libido

Well, this is just plain awful Are Antibiotics Ruining Your Libido? - The Daily Beast.  In this article, Robynne Chutkan argues that people's sex drives may be being ruined by antibiotics.  And she presents zero evidence for this other than handwaving.

Some things in this article that are inaccurate:
We’ve spent most of the last century figuring out how to eradicate our microbes, and we’re just now realizing that the vast majority are friends rather than foes that actually play a vital role in keeping us healthy.
No - the "vast majority" of microbes are not known to be our friends or to play a vital role in keeping us healthy.  Certainly, microbes and microbiomes do contribute to our health and well being.  But to say the "vast majority" are beneficial is, well, just silly.

How about this section:
Most of the patients I see suffer from manifestations of an imbalanced microbiome—a condition known as dysbiosis. Some of the signs and symptoms are localized to the GI tract, like bloating and gas; but others, including yeast infections, brain fog, fatigue, rashes, joint pain, anxiety, food cravings, allergies, and autoimmune disorders, reflect the universal role our microbes play in preventing disease
Well, based on this statement I would certainly recommend nobody see Dr. Chutkan for any of their medical treatment.  What exactly is the evidence "brain fog" is caused by dysbiosis?  Or fatigue?  Or anxiety?  Or food cravings?  (Yes, I agree that some of the other things listed have been shown to be affected by the microbiome, but each of these (e.g., allergies) is influenced by many many factors and as far as I know there are no scientific studies that show that one can look at people suffering from any of these ailments and determine if their microbiome has caused their problems or not.

And then there is the discussion of microbiomes, antibiotics and sex life:
And what’s more, a healthy, balanced microbiome is essential for a healthy, satisfying sex life.
But there’s another alarming, but hidden epidemic of dysbiosis that’s occurring, and it may be wreaking havoc on your sex life. It’s the common practice of taking antibiotics after intercourse to prevent urinary tract infections (UTIs).
She then goes on to discuss issues in cystitis and UTIs and infections and the vaginal microbiome.  Yes, the vaginal microbiome is important.  And yes, antibiotics and affects the vaginal microbiome, both in positive and negative ways.  So - I do think we should be concerned with overuse of antibiotics and how that affects microbiomes.  And we should be concerned with overuse in the context of UTIs.  But does that concern allow us to oversell the science?  I don't think so.  The worst part of this whole story relates to this issue:
If you’ve been using antibiotics to prevent post-coital UTIs and you’re finding that sex is less enjoyable than it should be, your vaginal microbes might be in need of some rehab. I recommend a three-pronged approach of avoidance, encouragement and repopulation
It may take some time before you see meaningful results, but this approach offers the possibility of real and lasting relief, rather than an antibiotic quick fix that ultimately ends up being ruinous to your sex life. 
The problem with this is that she presents no evidence that alterations int he microbiome affect libido or sex life and no evidence that her recommended solutions (e.g., probiotics and prebiotics) help with such symptoms.  So, yes, overusing antibiotics is a risk we should limit as much as possible.  But no, lets not glorify microbiomes and overcritique antibiotics by making people worry about their sex drive and sex life without evidence.  That is not helpful and could be harmful.  For this I am giving Robynne Chutkan a coveted overselling the microbiome award.

For more on this award see here.

Wednesday, September 02, 2015

From 1988 to 2015 - how Jennifer Doudna shaped my career (and now science and society)

Well, yesterday was really fun.

In college, I switched from being an East Asian Studies major to being a Biology major in my sophomore year but had no idea what aspect of biology I might focus on.

Then I took a course that changed my life. The course was taught by a PhD student at Harvard and it was a kind of supervised reading class. The course was a full year class with weekly meetings to discuss various papers and news stories and such.  The topic was "The Origin of Life: Catalysis in Evolution" and it covered things like chemical evolution, catalytic RNA, the RNA world, introns, Lamarck vs. Darwin, and more.   The course syllabus is posted below:

This course changed my life in multiple ways.

First, in the course I learned how to critically read scientific papers. A very important skill. And also I got introduced to the world of catalytic RNA and also the world of "Cairnsian Mutation" which became the topic of my grad. school applications, my NSF predoctoral fellowship application, and the first two years of my PhD work. And I also got introduced to the work of Norm Pace.

This led me to seek out ways to combine my interest in ecology and evolution with molecular biology, which in turn led me to joining the lab of Colleen Cavanaugh and starting work on culture independent DNA studies of microbes.

Anyway, I could go on and on. But this course was transformative. Over the years I had heard about the student who had taught the course and her work, but had not actually seen her in person until yesterday.

The course instructor was Jennifer Doudna. And yesterday I got to see her talk about her work on CRIPSR and CAS9 systems. She has already won a large number of prizes for her work on this, and likely more to come. I cannot say I am surprised. Though I had many teachers at Harvard who were famous, and some of whom were also great teachers and researchers, I can say without a doubt that the one who impressed me most was Doudna. Her passion for science, for biology, for teaching, for being critical while reading articles, and for just wild things that organisms do, was contagious. So cool to see what she is doing now.

Anyway - I made a Storify of the Tweets (mostly mine) from her talk. Check them out below:

UPDATE - found my term paper from the class . posting it here.

Thursday, August 27, 2015

A worthy cause: Help fund a "Patient Centered Probiotics Reference"

UPDATE 8/27/15 - May have had a brain cramp on this.  See comment from Richard Jefferson.  Not sure this is in fact a worthy cause.

As many know I expend a lot of energy railing against overselling of the microbiome. And one aspect of this is the misinformation that is out there regarding probiotics. Well, this looks like it might help provide an antidote to some of the BS that is out there: This is a crowdfunding effort to create a curated resource with information on scientific studies of probiotics.
Powered by FundRazr
From their site:
In his book, "Follow Your Gut", Dr. Rob Knight cited several examples of how your gut microbes can affect your mood, the functioning of your immune system and inflammatory diseases. He suggests that you consult your physician or pharmacist to recommend probiotics that have randomized, placebo controlled trials backing them or failing that, you can survey the latest research published in scientific journals yourself. I know this is not a simple task for the regular consumer. A master reference of probiotics that you can refer to when making decisions on what products to purchase would be a handy thing. Dr. Knight notes in his book, that " patient centered resource exists that compiles this data." If someone were to go ahead and do a google search for this information, you'd have to wade through a lot of marketing material from companies trying to sell you stuff. By focusing on the peer reviewed scientific literature, we eliminate all the marketing material. The research reports are then read and summarized by our scientists (curators) who put it in our reference database in a language you don't need to be an expert to undestand. My colleague, Dr. Stephan Schurer, of the University of Miami Medical School, and I have built databases as tools for researchers to search for new drugs. We built these by extracting & summarizing research published in scientific journals. We propose to use a similar approach to build the probiotics reference. The money we raise will go to purchasing subscriptions to the scientific journals (like Journal of Gastroenterology and Gut Pathology) so that we can download the relevant research articles. It also goes to pay the part time curators who will read the journals and enter the key information into the database and lastly it goes to the costs of hosting a website and licensing of necessary softwares. Please help us in any way you can. We greatly appreciate monetary pledges, but also we need you to tell your friends and spread the word about our project.
Definitely seems like a worth project

Wednesday, August 12, 2015

TWIMO: This week in microbiome overselling - how the microbiome destroyed the Ego, Vaccine Policy, and Patriarchy

Well.  I guess thanks are in order to my friend and colleague David Pollock who pointed me to this on Facebook and asked if it fit the mold for an Overselling the Microbiome Award: How The Microbiome Destroyed the Ego, Vaccine Policy, and Patriarchy.  And, well, it certainly does.  This is just so so so so so painful I do not really even know what to say.  So I am just going to quote some of the worst parts here for everyone to think about

A bold beginning

The relatively recent discovery of the microbiome is not only completely redefining what it means to be human, to have a body, to live on this earth, but is overturning belief systems and institutions that have enjoyed global penetrance for centuries.
 And more boldness

A paradigm shift has occurred, so immense in implication, that the entire frame of reference for our species' self-definition, as well as how we relate fundamentally to concepts like "germs," have been transformed beyond recognition
Got to invoke some Copernicus

a Copernican revolution when it comes to forming the new center, genetically and epigenetically, of what it means in biological terms to be human
A little side throw at vaccines

This concept is of course intellectually infantile, and if you do some investigating you'll find it was never quite grounded in compelling evidence or science.
And of course, the patriarcy must be attacked too

The microbiome has also fundamentally displaced a latent patriarchal prejudice concerning the relative importance and contribution of the man and woman towards the health and ultimately the continuation of our species.
And the microbiome is clearly trying to counter the patriarchy

it follows that most of our genetic information as holobionts is maternal in origin. 

if 99% of what it means to be human is microbiome-based, and if the mother contributes most, if not all, of the original starting material, or at least the baseline and trajectory of future changes in the inner terrain, then her contribution becomes vastly more important than that of the father.

This is perhaps the best part:

In other words, being born in a hospital via C-section and vaccination, will produce, genetically and epigenetically, a human that is so different – qualitatively – from one born at home, naturally, that they could almost be classified as different species, despite sharing nearly identical eukaryotic DNA (remember, only 1% of the holobiont's total). 
And let's attack men some more

In light of the new, microbiome-based view, the male role in protecting the health of women and children will be irrevocably downgraded in importance, not just professionally and medically, but biologically.
And then, well, this

The birth process, also, has been described as the closest thing to death without dying (it is ironic that anesthesiology, which could also be described in the same way, makes obstetrical interventions like C-section and epidural possible, at the same moment that it negates the spiritual experience of natural birth/women's empowerment we are describing), offering women a window into the 'in between' and a direct experience of Source that men, less likely to experience it naturally would later emulate and access through the various technologies of shamanism.
And all of this then justifies environmental protection

This means we can't simply live in a hermetically sealed bubble of shopping for organic, non-GMO certified foods at Whole Foods, while the entire planet continues to go to post-industrial hell in a hand basket.  Our responsibility becomes distributed across everything in the world, and every impactful choice then becomes relevant to the fundamental issue and imperative at hand. With the microbial biodiversity in Big Ag, GM-based agricultural zones fire-bombed with biocides, by the very same corporations that either own or distribute the "organic brands" we all love to think will save our bodies, if not the planet, we need to step deeper into our activism by stepping out of the diversions and palliative measures that don't result in lasting change.
 I think the words speak for themselves.  But not for me.  Or my microbes.

Tuesday, July 28, 2015

YAMMA - Yet Another Mostly Male Award - AAAS Public Engagement Award

So - I saw an post on Twitter about the AAAS Public Enagement with Science Award

And I went to check it out since, well, I wondered - how could I win that.  And so I thought - I should look at how I compare to previous winners.  And in one way I compare really well. I am male.

Below is a list of past winners (via AAAS). In yellow I highlight those that appear to be male and green those that appear to be female. I note I base my assignment on appearance and names and descriptions of the people including the descriptions from AAAS. I realize that determining someone's gender is not always straightforward and that there are people who do not fit into this binary gender division and I apologize for any mistakes made.
  • 2014 James Kakalios 
  • 2013 Steven Strogatz
  • 2012 Richard B. Alley
  • 2011 Nalini Nadkarni
  • 2010 J. John Cohen
  • 2009 May R. Berenbaum
  • 2008 Kenneth R. Miller
  • 2007 Neil deGrasse Tyson
  • 2006 S. James Gates, Jr.
  • 2005 Jane Lubchenco
  • 2004 Eric S. Lander
  • 2003 John Allen Paulos
  • 2002 Bassam Shakhashiri
  • 2001 Ian N. Stewart
  • 2000 Vaclav Smil
  • 1999 Lawrence Krauss
  • 1998 Christopher Wills
  • 1997 Barry T. Peterson
  • 1996 Alan J. Friedman
  • 1995 Carl Sagan
  • 1994 Edward O. Wilson
  • 1993 Science Theatre
  • 1992 Farouk El-Baz
  • 1991 Stephen H. Schneider
  • 1990 William L. Rathje
  • 1989 Robert D. Ballard
  • 1988 Anthony M. Fauci
  • 1987 Philip Morrison
The totals are 24 men and 3 women (and one group).  Or, for those assigned to a gender, 89 % men and 11 % women.  Could this all be about merit?  I don't think so.  I think there are many examples of areas in which AAAS has problems with gender bias.  For example, consider the recent letter (of which I am a cosigner) regarding AAAS' reinforcement of "damaging stereotypes".

Sunday, July 26, 2015

Possibly the worst press release on the microbiome ever: Greenlaw and Ruggiero and the third brain.

Well, this is a combination of horrendous, frustrating and painful: Discovery of Microbiome “Third Brain” Confirmed by Scientific Research in Japan | Business Wire. This is a press release that focused on Peter Greenlaw and Marco Ruggiero so I assume it came from him.

It starts off discussing a new paper from
"the prestigious peer-reviewed scientific Journal “Anticancer Research
which according to the PR:
"describes the properties of a food product that is reminiscent of the “super food for the third brain.”  
Note - no link is provided to the paper.  Not surprisingly, the PR then transitions to being something else - in this case a new book by Greenlaw:
 "this finding supports the discoveries revealed in the book “Your Third Brain,” co-authored by Peter Greenlaw, Dr. Marco Ruggiero and Drew Greenlaw, with the forward written by author John Gray, Ph.D." 
So this is not really about the new paper - this is a kind of bait and switch. Then comes one of the doozies "
Four and a half years ago, a huge discovery was made. In 2010, a team of researchers discovered a new organ that had gone undetected for more than 3,000 years in Human Anatomy. They called this newly discovered organ the microbiome.

What?  The human microbiome was discovered four and a half years ago?  That is of course complete BS.  I note - there is something a tad bit off here with the "3000 years too".  Is this a religious reference of some kind?

Then comes another amazing section.  Underlining by me
The microbiome is much more than the gut microflora. It is a complex organ that is responsible for the development and function of all the other organs and systems, from the brain inside our heads to the immune system. The influence of the microbiome, that is located all over our body and not only inside the gut, on our behavior and intellectual functions is so significant that it can be aptly named “the third brain” as it is described in the book.
Wow.  I mean sure there is some evidence that the human microbiome can impact the brain.  But first of all, it is ridiculous to consider it "the third brain".  Also, to say it is responsible for the development of the rest of the body is just plain silly.

How about this next section?
Dr. Ruggiero’s team is working hand in hand with the complete cooperation and unprecedented collaboration of medical doctors, with the goal of extending the highest possible quality of life for their patients for as long as possible. And although Dr. Ruggiero did not personally discover the microbiome, he did identify it as the third brain.
OK - so is this meant to imply other people don't collaborate with medical doctors?  And other people do try to extend quality of life for parients?  

So many other bad sections I am not sure which other ones to point out.  How about this:
Before this book was written, man did not know that his thoughts, feeling, emotions, behaviors, his supposed free will were under the control of a non-human organ whose existence had gone undetected until very recently, the microbiome.
This sounds like the voice over you might have in a science fiction horror movie.  Except - this is real fiction and from a horror show of a press release. 

I must say - Greenlaw and Ruggiero are clearly very proud of themselves.  I will just leave everyone with the last paragraph for people to ponder how humble and understated it is.
This book describes what is and how we can take control of this non-human third brain and aspire to bring out the superman that is inside us. As the Philosopher wrote: ‘Let your will say: the overman shall be the meaning of the earth... Man is a rope, tied between beast and overman—a rope over an abyss ... what is great in man is that he is a bridge and not an end.’ Thanks to the information contained in this book, for the very first time in the history of mankind we can transform ourselves and reach this end
I am hereby awarding Greenlaw and Ruggiero an "Overselling the Microbiome" award.  But that seems too small for them.  They deserve some sort of "Biggest pile of BS ever" award.  I will consider starting such a new award series in their honor.