Tuesday, September 30, 2014

Today on "Express Yourself" Teen Radio - me - being interviewed about #Microbes & #OpenScience

Just a little self-centered plug.  I was interviewed recently for Express Yourself! | VoiceAmerica™ teen radio show.  The teens interviewing me included Henna Hundal who worked in my lab this summer as an intern on our "Seagrass Microbiome" project. See a post from Cassie Ettinger about Henna's work.  Also see:

It was a fun interview and I love the idea of teens doing a science radio show.   From their site
Science is everywhere. From the stars that light the night sky to the intricate patterns on a butterfly’s wings, science is at play in all parts of our world and is continually making our lives so great. Hosts Henna Hundal and Courtney Chung discuss how science shapes our perspective on life from cell phones to lawn mowers, from cures for diseases to prosthetic limbs. Global Youth Talk reporter, Ryan Sim, talks about science careers in the United Nations, and how this international community is looking at science innovation to create solutions for the next generation. Special guest Dr. Jonathan Eisen,a Full Professor at the University of California, Davis, with appointments in the UC Davis Genome Center, the School of Medicine, and the College of Biological Sciences focuses on communities of microbes and how they provide new functions - to each other or to a host. Dr. Eisen is entertaining with his study systems of boiling acid pools, surface ocean waters, agents of many diseases, and the microbial ecosystems in and on plants and animals. In Health with Henna, Henna Hundal reports on how we can prevent the negative effects of prolonged sitting. It’s important to take those “stretch breaks” every hour. Whether it’s writing scientific articles, thoughtful science reporting, or even talking about science on the radio, integrating humanities with science is key to reaching a mass audience.
So - I recommend everyone listen ...12 noon Pacific Time on VoiceAmerica Kids Channel. Express Yourself! | VoiceAmerica™


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Monday, September 29, 2014

Personalized Medicine World Conference 2015: 55 speakers 7 of which are women #YAMMM #StemWomen

Well, umm, Ralph Snyderman, despite the email invitation I will not be attending PMWC 2015 Silicon Valley.  Why not?  Well how about the fact that you have 55 speakers listed, only 7 of which are women.






Previous year's meetings are not much better.  For example, for the 2014 Meeting in Silicon Valley the Track 1 session (which they call the premier session or something like that) has a ratio of 52:5 Male:Female.


Wednesday, September 24, 2014

#YAMMM Alert: Drug Discovery and Therapy World Congress, a meeting made for @realDonaldTrump & other men

Elizabeth Bik sent me a link to this meeintg: DRUG DISCOVERY & THERAPY WORLD CONGRESS 2015 with a comment about the ratio of males to females in the keynote speakers.  And it is painful.  Of the plenary and keynote speakers, 15 are male and 1 is female.  Below I show pics of the plenary and keynote speakers:

Plenary and Keynote Speakers at Drug Discovery and Thearpy World Congress

Female Plenary and Keynote Speakers at Drug Discovery and Thearpy World Congress
Two bonus people who could have been giving keynote talks but who actually are not.

The gender bias at this meeting puts into perspective the push by the NIH to get drug researchers to inlcude more female subjects in their studies.  See for example, Why Are All the Lab Rats Boys? NIH Tells Drug Researchers to Stop Being Sexist Pigs.  Here is a thought, maybe we can get some of these speakers to cancel speaking at the meeting and also maybe we can get nobody to attent the meeting.  Sigh.  Yet another mostly male meeting.  Also known as "YAMMM".


Tuesday, September 23, 2014

Triclosan in toothpaste: potential risks are not a "rumor" as arrogant Colgate official argues, but are something to worry about

Triclosan in my toothpaste (and maybe yours too)
I was reading some posts of a friend and went down a bit of a rabbit hole that led me to a place that did not make me happy.

First I saw a post about some issues with Crest Toothpastes containing polyethylene: Dentist calls Crest toothpaste dangerous; Now P&G changing ingredients.  This seemed a bit disturbing.  But then I saw a "Related Link": Shoppers Ditching Colgate Total Amid Triclosan Fears.  And I thought - holy cra*## - really? I had no idea triclosan was in toothpaste.  And why did I react strongly?  Well triclosan, which is antimicrobial agent, though it has it's potential benefits, has some potential risks associated with it's antibacterial activity (see also this discussion from the EU).  What are these possible risks?  Risks like increasing the frequency and spread of antimicrobial resistance.  And risks like messing with microbial ecosystems.

And due to these potential risks, I have been blogging and writing and complaining about the use of triclosan in various building materials for some time now.  For example

And also see:

Story Behind the Paper: Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads (by Rogan Carr and Elhanan Borenstein)

Here is another post in my "Story Behind the Paper" series where I ask authors of open access papers to tell the story behind their paper.  This one comes from Rogan Carr and Elhanan Borenstein.  Note - this was crossposted at microBEnet.  If anyone out there has an open access paper for which you want to tell the story -- let me know.


We’d like to first thank Jon for the opportunity to discuss our work in this forum. We recently published a study investigating direct functional annotation of short metagenomic reads that stemmed from protocol development for our lab. Jon invited us to write a blog post on the subject, and we thought it would be a great venue to discuss some practical applications of our work and to share with the research community the motivation for our study and how it came about.

Our lab, the Borenstein Lab at the University of Washington, is broadly interested in metabolic modeling of the human microbiome (see, for example our Metagenomic Systems Biology approach) and in the development of novel computational methods for analyzing functional metagenomic data (see, for example, Metagenomic Deconvolution). In this capacity, we often perform large-scale analysis of publicly available metagenomic datasets as well as collaborate with experimental labs to analyze new metagenomic datasets, and accordingly we have developed extensive expertise in performing functional, community-level annotation of metagenomic samples. We focused primarily on protocols that derive functional profiles directly from short sequencing reads (e.g., by mapping the short reads to a collection of annotated genes), as such protocols provide gene abundance profiles that are relatively unbiased by species abundance in the sample or by the availability of closely-related reference genomes. Such functional annotation protocols are extremely common in the literature and are essential when approaching metagenomics from a gene-centric point of view, where the goal is to describe the community as a whole.

However, when we began to design our in-house annotation pipeline, we pored over the literature and realized that each research group and each metagenomic study applied a slightly different approach to functional annotation. When we implemented and evaluated these methods in the lab, we also discovered that the functional profiles obtained by the various methods often differ significantly. Discussing these findings with colleagues, some further expressed doubt that that such short sequencing reads even contained enough information to map back unambiguously to the correct function. Perhaps the whole approach was wrong!

We therefore set out to develop a set of ‘best practices’ for our lab for metagenomic sequence annotation and to prove (or disprove) quantitatively that such direct functional annotation of short reads provides a valid functional representation of the sample. We specifically decided to pursue a large-scale study, performed as rigorously as possible, taking into account both the phylogeny of the microbes in the sample and the phylogenetic coverage of the database, as well as several technical aspects of sequencing like base-calling error and read length. We have found this evaluation approach and the results we obtained quite useful for designing our lab protocols, and thought it would be helpful to share them with the wider metagenomics and microbiome research community. The result is our recent paper in PLoS One, Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads.

The performance of BLAST-based annotation of short reads across the bacterial and archaeal tree of life. The phylogenetic tree was obtained from Ciccarelli et al. Colored rings represent the recall for identifying reads originating from a KO gene using the top gene protocol. The 4 rings correspond to varying levels of database coverage. Specifically, the innermost ring illustrates the recall obtained when the strain from which the reads originated is included in the database, while the other 3 rings, respectively, correspond to cases where only genomes from the same species, genus, or more remote taxonomic relationships are present in the database. Entries where no data were available (for example, when the strain from which the reads originated was the only member of its species) are shaded gray. For one genome in each phylum, denoted by a black dot at the branch tip, every possible 101-bp read was generated for this analysis. For the remaining genomes, every 10th possible read was used. Blue bars represent the fraction of the genome's peptide genes associated with a KO; for reference, the values are shown for E. coli, B. thetaiotaomicron, and S. Pneumoniae. Figure and text adapted from: Carr R, Borenstein E (2014) Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads. PLoS ONE 9(8): e105776. doi:10.1371/journal.pone.0105776. See the manuscript for full details.
The performance of BLAST-based annotation of short reads across the bacterial and archaeal tree of life using the 'top gene' protocol. See the manuscript for full details. Figure and text adapted from: Carr R, Borenstein E (2014) Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads. PLoS ONE 9(8): e105776 


Saturday, September 20, 2014

Notes from 2007 for a blog post I should have written: How many microbial cells in humans?

Well sometimes you just screw up.  In 2007 I attended some planning meetings for the human microbiome project (see for example A human microbiome program? a post I wrote from one of the meetings in 2007).  And at those meetings I kept asking one question.  Where did this "fact" everyone kept citing that there were "10 times as many microbial cells in the human body as there were human cells" come from?  I could not find a citation.  So I started taking some notes for a blog post about this.  Here are those notes:

Wikipedia linkOnline textbook hereSears paper from Arizona site. She discusses only gut bacteria and cites a Gordon paper from 2001.
Seems to not be from this paper but really from here:
This in turn is not from there but apparently here

But, alas I got distracted.  And I did keep asking people - where did this "fact" come from.  And most people just brushed me off (and probably thought I was a bit of a crank ...). And nobody had a good answer.  Well, I was both pleased and sad (because I should have done it) to see Is your body mostly microbes? Actually, we have no idea by Peter Andrey Smith in the Boston Globe who addresses this issue in much much more detail that I ever could have done.  Everyone who works on the human microbiome and who is interested in "facts" and how they can get misreported should read this.  As a side note, Smith reports in the article that this is even given as a fact in Ted talks.  Sadly mine was one of them.  This is despite the fact (yes, the fact) that I swore to myself that I would NOT say that in my talk since I have been such a crank about this issue at meetings.  OMG - such truisms are so pervasive that even someone who actively questioned the truism still used it.  Uggh.  Oh well.  I really should have finished that draft post.

Friday, September 19, 2014

Don't forget to positively highlight meetings w/ "good" gender ratio of presenters

As many know, I spend a decent amount of effort critiquing conferences that have poor speaker diversity (mostly focus on gender ratio).  Well I am also trying to start calling out in a positive way those meetings that do a good job with speaker diversity. And here is one: 2014 Xenopus Genetics meeting in Pacific Grove.  I was pointed to it in an email that was in response to a Tweet I posted (not sure if I have permission to say who this was from - will post if they say it is OK). (UPDATE 9/20 - it was Ian Quigley).
From what I compute - the ratio was 30:22 male: female.  I do not know what the ratio of the "pool" of speakers is but regardless, having 42% female speakers is a more even ratio than I have seen for most life sciences meetings.  So they deserve some props for this.

Female speakers highlighted in yellow.  Male in green.  

Keynote Lecture: Rebecca Heald

Special Lectures from John Gurdon and Marc Kirschner

Invited Speakers

Enrique Amaya, University of Manchester

Ruchi Bajpai, University of Southern California

A distasteful & disgraceful "Are there limits to evolution?" meeting at the University of Cambridge #YAMMM

Well, I saw this Tweet the other day
And though there was a bit of a discussion on Twitter I felt I had to follow up with a blog post. When I saw the post I was at a conference (Lake Arrowhead Microbial Genomes) where I could get Twitter access but for some reason very little web access. So I could not dig around until now (I am home). 

This meeting is a complete disgrace and an embarassment for the field of evolutionary biology, for the University of Cambridge which is hosting the meeting, and for the Templeton Foundation which is sponsoring it.

Why do I say this? Well, pretty simple actually. The meeting site lists the Invited Keynote speakers for the meeting.  Notice anything?  How about I help you by bringing all the pictures together.


Notice anything now?  How about I help you some more by masking out the men and not the women.


Impressive no?  25 speakers - 23 of them male.  I guess that means there are no qualified female speakers who coudl discuss something about evolution right?  It would be worth reading "Fewer invited talks bu women in evolutionary biology symposia" to get some context.  What an incredible, disgusting, distasteful and disgraceful meeting.  

I recommend to everyone who was considering going to this meeting - skip it.  Also consider writing to the University of Cambirdge and the Templeton Foundation to express your thoughts about the meeting.  This certainly is a fine example of Yet Another Mostly Male Meeting (YAMMM).  Well, maybe I should word that differently - this is a disgusting example of a YAMMM.  


For more on this and related issues



  • Posts on Women in STEM


  • Also see


    Sunday, September 14, 2014

    Everything You Wanted to Know about the Lake Arrowhead Microbial Genomes meeting #LAMG14

    The Lake Arrowhead Microbial Genomes meeting, which happens every other year, is starting tonight.  I love this meeting.  No bias here since I am now a co-organizer.  But I really love this meeting.  I am posting here some background information about the meeting for those interested.  We will be live tweeting the meeting using the hashtag #LAMG14.  This years program is here.

    Posts of mine about previous meetings
    Blog posts by others
    Programs and notes from past meetings
    Meeting Web Sites
    I have uploaded slides from my previous presentations at the meeting
























    Friday, September 12, 2014

    Fun read of the day: On whimsy, jokes, and beauty: can scientific writing be enjoyed?

    This is such a fun paper: On whimsy, jokes, and beauty: can scientific writing be enjoyed? by Stephen Heard in Ideas in Ecology and Evolution 7: 64–72, 2014  I found out about it in an email from Heard, who sent it to me because he had earlier commented on a blog post I had written: The best writing in science papers part 1: Vladimir Nabokov in Notes on Neotropical Plebejinae (Lycaenidae, Lepidoptera).

    Anyway - enough about me - what about this paper?  It has so many nuggets of interest I am not sure which to highlight so I will just go through some of it.  Oh - and it is published with a Creative Commons Attribution license (yay).
    Abstract: While scientists are often exhorted to write better, it isn’t entirely obvious what “better” means. It’s uncontroversial that good scientific writing is clear, with the reader’s understanding as effortless as possible. Unsettled, and largely undiscussed, is the question of whether our goal of clarity precludes us from making our writing enjoyable by incorporating touches of whimsy, humanity, humour, and beauty. I offer examples of scientific writing that offers pleasure, drawing from ecology and evolution and from other natural sciences, and I argue that enjoyable writing can help recruit readers to a paper and retain them as they read. I document resistance to this idea in the scientific community, and consider the objections (well grounded and not) that may lie behind this resistance. I close by recommending that we include touches of whimsy and beauty in our own writing, and also that we work to encourage such touches in the writing of others.
    OK - the title would have drawn me in anyway but the abstract definitely had me.
    If scientific writers aren’t sure how to write better, it isn’t for lack of advice. Dozens of guidebooks discuss form, style, and goals in scientific writing (e.g., Montgomery 2003, Davis 2005, Day and Gastel 2006, Katz 2006, Matthews and Matthews 2007, Rogers 2007, Harmon and Gross 2010, Hofmann 2010, Pechenik 2010, Greene 2013, Heard unpubl.).
    OK - I am going to have to look at some of these.

    Heard documents a bit of a spat between Sprat and Boyle from the 1660s regarding scientific writing.  I especially like the Boyle quote:
    To affect needless rhetorical ornaments in setting down an experiment...were little less improper than...to paint the eyeglasses of a telescope...in which even the most delightful colours cannot so much please the eye as they would hinder the sight...And yet I approve not that dull and insipid way of writing, which is practiced by many...for though a philosopher need not be solicitous that his style should delight his reader with his floridness, yet I think he may very well be allowed to take a care that it disgust not his reader by its flatness...Though it were foolish to colour...the glasses of telescopes, yet to gild...the tubes of them may render them most acceptable to the users (Boyle 1661:11-12, spelling and punctuation modern- ized).
    Heard then goes through some different aspects of good scientific writing
    • Sightings (1): Playfulness in the scientific literature
    • Sightings (2): Beauty
    Also - he then doscusses pushback against the "notion that whimsy, jokes, and beauty can have a place in our scientific literature." which I have also seen in many contexts.

    He ends with suggestions and I quote the whole section with some highlights:
    If you write papers that are crystal clear and thus effortless to read, you’ll have achieved the primary goal of scientific writing and your work will be among the best of our literature. But if you want to reach for even more, if you agree with me that we can also offer our readers some pleasure in reading, what can you do? To begin, you can try to write with small touches of whimsy, humanity, humour, and beauty—without, of course, compromising clarity; and even knowing that sometimes, reviewers will make you take them out. I am not suggesting writing in which art shares the stage equally with content (as can be true in the lay literature). Rather, the goal that’s within our reach is clear, functional writing punctuated with occasional nuggets of playfulness or glints of beauty—to extend Boyle’s metaphor, not a telescope of solid gold but one lightly gilded. 
    You can also work to encourage pleasure in what your colleagues write, in two complementary ways. First, when you review manuscripts, you can suppress the reflex telling you to question any touches of whimsy, humour, or beauty that you find; you can even (gently) suggest some be put in. Second, you can announce your admiration of writing that has given you pleasure. Announce your admiration to the writers who crafted the passage, to editors who might be considering its fate, and to students or colleagues who might read it. If we choose to, we can change our culture to deliver, and value, pleasure along with function in our writing.
    This is a must read paper.  And I really wish more people would endorse the idea that scientific writing can include more than just science.  Of course, there are many who already endorse this notion but for those who do not - give it a try.