Friday, October 28, 2016

A gloomy day at the #UCDavis Genome Center Halloween Symposium - a model for a #manel #yammm

It is a gloomy day, at least for me, at #UCDavis today.

Yes it is raining and cloudy.  But that is not the gloomy part. I like rain and clouds and we don't get enough of either around here. The issue for me is the Symposium happening today in my building.  Run by the UC Davis Genome Center, which I am a part of.  What is the problem?

Well here is the flier

That is nine presenters.  Eight of which are men. 
  • S. Dinesh-Kumar
  • Brett Phinney
  • Anthony Herren
  • Jessica Franco
  • Jack Cuniff
  • John Yates
  • John Muchena
  • Ilias Tagkopoulos
  • Nuno Bandeira

That comes to 11% female speakers.  Not a good ratio.  But you know this is just one sample right?  It could be a random anomaly, or something else.

So - lets look at last years Halloween symposium.

That is five speakers, all men.

  • Mingcheng Luo UC Davis
  • Chris Streck 10X
  • Marco Blanchette Dovetail
  • Matthew Seetin PacBio
  • Matthew Settles, UC Davis

Four speakers. All male.

  • Bruce Draper UC Davis, Molecular and Cellular Biology
  • Bruce Conklin, Gladstone Institute of Cardiovascular Disease, UCSF
  • David Segal, UC Davis, Genome Center
  • Dana Carroll, University of Utah, Department of Biochemistry

So over the last three years we have 94% male presenters. It is a better if you go back further. 2013 was 50-50.  2012 was  ~ 70-% male.  2011 was  55:45 or so.  But over the last three years something has devolved.  And no, I will not be attending.  And yes, I have made comments about this, but maybe too few.  

It is so frustrating to keep seeing this happening over and over in academia and science.  And to see it so close to home, well, it is really extraordinarily disappointing. 

I sent the organizers which I think has some great examples of how to run a diverse meeting.

Below are some articles worth looking at on the topic. 

I certainly feel partially responsible for this, because it is in my building and run by my Center.   Now I had nothing to do with this even, but still ...  I will do my best to make sure this does not happen ever again at the UC Davis Genome Center.  But I will not be attending this year's meeting.  

Monday, October 17, 2016

Thanks to all for "Suggestions for 11 year old daughter who wants to learn to code"

I am so thankful to the whole community out there who gave answers to my request for suggestions for my 11 year old daughter who wants to learn to code.

Today we were both home sick and when she said she was bored she then asked if we could try some of the examples people suggested.  And we ended up playing around with Python at Codeacademy and she spent hours on it.  So much fun. See below:

No - #FFS - no - I will not speak at your meeting given the lack of diversity of speakers

So a few days ago I got asked to do a paid speaking engagement for a meeting

Dear Dr. Eisen,

I hope this email finds you well!

We have a client that's interested in you speaking at their Autoimmune Conference in New York on March 24, 2017

Do you have a standard speaking fee/range that I can report back to my client?  If you're able to confirm your availability as well, that would be great!

The audience would be primarily physicians. 

Your consideration is very much appreciated!


Sounded nice - getting paid to go to New York.  What could go wrong right?. Then I did some Googling to find out about the meeting.  Found it - the Interdisciplinary Autoimmune Summit: And, as I do for all meeting invites these days, I looked at their speaker line up.  For this years and previous years.  And well, I was not impressed.

A lot of men.  Men men men and men. So I wrote back

Friday, October 07, 2016

Matt Hahn @3rdreviewer talk at #UCDavis - pen and paper notes

Matt Hahn was at UC Davis giving a talk yesterday.
I did not have my laptop available so took notes with - gasp - a pen and paper.  I thought it was quite a nice talk so am posting my notes here.  More about Matt and his work can be found here:

Thursday, October 06, 2016

The White Men's Microbiome Congress #YAMMM #Manel #Boycott

So I got this email this morning inviting me to attend a conference: the Second Annual Human Microbiome Congress in San Diego. (also called the North American Microbiome Congress).

And it struck me that all the featured speakers were men.

 Great.  So I decided to give them the benefit of the doubt, hoping that maybe if I looked at the rest of the speakers it would be better.

So I had to register on some web site to download the full agenda for the meeting.  And there were the featured speakers, rippling with diversity

So then I went to scroll through the document looking for the other speakers.

OMFG - what a joke.

Sunday, October 02, 2016

Yet another biased meeting from Oxford Global - their meetings should be shunned #YAMMM #GenderBias

Well, Oxford Global has done it again.  They have found a way to be one of the most extremely gender biased conferences around.  Their 2016 Genome Editing Congress Speakers. Their web site lists 20 speakers, 19 of which are men.  (One of the men is listed twice - I am not sure if that is due to giving two talks or a mistake.  So this may be 19 speakers~ 95, 18 of which are men).  Regardless that comes to ~ 95% male speakers.

  • Andre Choulika, CEO Cellectis
  • Guna Rajagopal, VP – Global Head, Computational Sciences, Discovery Sciences Janssen
  • Lorenz Mayr, VP & Global Head, Reagents & Assay Development Astrazeneca
  • Zheng-Yi Chen, Associate Professor Harvard Medical School
  • Daniel Anderson, Associate Professor MIT
  • Marcello Maresca, Associate Principal Scientist Astrazeneca
  • John Doench, Director; Associate Director, Genetic Perturbation Platform Broad Institute
  • Chad Cowan, Associate Professor  Harvard
  • Pablo Perez Pinera, Associate Professor University of Illinois
  • Jim Collins, Professor MIT
  • Channabasavaiah Gurumurthy, Director, Transgenic Core Facility University of Nebraska Medical School
  • Danilo Maddalo, Senior Scientist and Lab Head Novartis Institutes for BioMedical Research
  • Rodolphe Barrangou, Associate Professor North Carolina State University
  • Stephanie Mohr, DRSC Director Harvard Medical School
  • Robert Howes, Associate Director MedImmune
  • Channabasavaiah Gurumurthy, Director, Transgenic Core Facility University of Nebraska Medical Center
  • James Carothers, Assistant Professor University of Washington
  • William Theodorus Hendriks, Instructor in Neurology Harvard Medical School
  • Mark Osborn, Assistant Professor University of Minnesota
  • Jeff Chamberlain, Professor University of Washington
1 and 19 were counted at Genome Editing USA Congress #OxfordGlobal. Learn more at GenderAvenger Tally

Sponsors of the meeting should be contacted about this:

Sadly this is a consistent pattern for Oxford Global. See for example Oxford Global Sequencing Meetings: Where MEN Tell You About Sequencing #YAMMM and also Time to boycott Oxford Global meetings due to blatant sexism

Really - we need as a community to stand up to these types of meetings.  Oxford Global meetings should be boycotted.  And the companies that sponsor their meetings are complicit in their gender bias.

UPDATE  10/2 12:56 PM - decided to look at another one of their meetings that is linked from this one

2nd Annual Next Generation Sequencing USA Congress
3-4 October 2016, Boston, USA

83 % male speakers.  Grand.

  • James Knight, Director of Bioinformatics Yale University
  • John Quackenbush, Professor Dana-Farber Cancer Institute
  • Shanrong Zhao, Director Pfizer Inc.
  • Nazneen Aziz, Research Professor Arizona State University
  • George Weinstock, Director and Professor Jackson Laboratory for Genomic Medicine
  • Alexander Wait Zaranek, Director Informatics Harvard Medical School
  • Rong Mao, Medical Director, Molecular Genetics and Genomics, ARUP Laboratories; Associate Professor, Pathology University of Utah School of Medicine
  • Mark Gerstein, Albert L Williams Professor of Biomedical Informatics, Molecular Biophysics & Biochemistry, and Computer Science Co-Director of the Yale Program in Computational Biology & Bioinformatics
  • James Willey, Professor of Medicine and Pathology University of Toledo
  • Neil R. Smalheiser, Associate Professor in Psychiatry University of Illinois College of Medicine
  • Mark Borodovsky, Regents’ Professor Georgia Tech
  • Scott J. Tebbutt, Associate Professor & Chief Scientific Officer University of British Columbia & PROOF Centre of Excellence
  • Michael Fraser, Program Director, Cancer Genomics, Radiation Medicine Program Princess Margaret Cancer Centre
  • Justin Johnson, Associate Director and Principal Scientist AstraZeneca
  • Leonora Balaj, Instructor in Neurology Massachusetts General Hospital Harvard Medical School
  • Aleksandra Markovets, Senior Scientist AstraZeneca
  • Baohong Zhang, Director of Clinical Bioinformatics Pfizer, Inc.
  • Steven Hart, Assistant Professor of Biomedical Informatics Mayo Clinic
  • Manolis Kellis, Professor and Head, MIT Computational Biology Group MIT
  • John Methot, Head of Scientific Computing Biogen
  • Andrew Hollinger, Associate Director: Scientific Communications Broad Institute
  • Yingtao Bi, Senior Manager in Statistics Abbvie Bioresearch Center
  • Paul Blainey, Assistant Professor of Biological Engineering, MIT and Core Faculty Member Broad Institute of MIT & Harvard
4 and 19 were counted at #oxfordglobal. Learn more at GenderAvenger Tally

For other posts on STEM Diversity see here.

Saturday, September 24, 2016

Wrap up from Gender Bias Under the Microscope Symposium #RFUSymposium #GenderBias

Had an amazing time at Rosalind Franklin University for their Gender Bias Under the Microscope Symposium. I made a Storify about it here:

For other posts on STEM Diversity see here.

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.

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 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

Saturday, July 09, 2016

A path towards the extinction of "Impact Factor"

From Ewen Callaway in Nature News:

Beat it, impact factor! Publishing elite turns against controversial metric : Nature News & Comment

Best part - the news from ASM

"And in an editorial that will appear on 11 July in eight of its journals, the American Society for Microbiology in Washington DC will announce plans to remove the impact factor from its journals and website, as well as from marketing and advertising. 
“To me, what’s essential is to purge the conversation of the impact factor,” says ASM chief executive Stefano Bertuzzi, a prominent critic of the metric. “We want to make it so tacky that people will be embarrassed just to mention it.”

This is in relation to the recent preprint I posted about a few minutes ago ...

Worth a read: A simple proposal for the publication of journal citation distributions

Worth a read: A simple proposal for the publication of journal citation distributions

This paper in BioRXiv is definitely worth checking out. Abstract is below:
Although the Journal Impact Factor (JIF) is widely acknowledged to be a poor indicator of the quality of individual papers, it is used routinely to evaluate research and researchers. Here, we present a simple method for generating the citation distributions that underlie JIFs. Application of this straightforward protocol reveals the full extent of the skew of distributions and variation in citations received by published papers that is characteristic of all scientific journals. Although there are differences among journals across the spectrum of JIFs, the citation distributions overlap extensively, demonstrating that the citation performance of individual papers cannot be inferred from the JIF. We propose that this methodology be adopted by all journals as a move to greater transparency, one that should help to refocus attention on individual pieces of work and counter the inappropriate usage of JIFs during the process of research assessment.
Source: A simple proposal for the publication of journal citation distributions | bioRxiv

(crossposted at the ICIS Blog)

Thursday, July 07, 2016

Agilent - where men are thought leaders

Well this is disappointing.  Was googling for a person and found this Agilent "Thought Leaders Program".  It is described as
This invitational program promotes fundamental scientific advancements by contributing financial support, products and expertise to the research of influential thought leaders in the life sciences, diagnostics, and chemical analysis.
Alas it might be described better as "Agilent Male Thought Leaders Program". In my estimation (based on the pronouns used in the descriptions of the people and in Googling around for more information), of the 31 "thought leaders" 28 are male.  That comes to a bit more than 90%.  It seems like there is some sort of bias here.   Agilent should and could do better.

Sunday, July 03, 2016

Blast from the past - Stephen Jay Gould on the "Planet of the Bacteria"

An influential article in my career development was this piece on the Washington Post in 1996 by Stephen Jay Gould. I was already convinced bacteria were important and interesting.  But it was nice to see the person who got me interested in evolution (via his books and then a class I took from him in college) emphasizing the bacteria.  Here is a link to the Post archive of it.

PLANET OF THE BACTERIA - The Washington Post

Well, my mom sent me a copy of it and I kept it all these years.  Just scanned it so, I thought I would share what it looked like in the paper since this is VERY different from looking at the text on the Post archive site.

I like the last part too - an ad for the American Society for Microbiology that went with the article. 

Friday, May 13, 2016

Pleasantly surprised by the National Microbiome Initiative

So I got this email a few weeks ago inviting me to the White House.

Not every day that I get invited to the White House.  And I thought I was probably on their shit list after removing my name from the "Unified Microbiome Initiative" paper due to it being non open access.  So I asked a colleague if she could teach in my large introductory biology class for me on May 13 and she said yes.  So I RSVP to the meeting and told my mom I would be coming to the DC area (where I grew up).  And I told everyone, proudly "I am going to the White House".

I realized I had a tight schedule for flying in and out since I had to be back in Davis Saturday AM.  So I wrote to the White House to ask about the schedule for the event.  You see, I had no information as to what this event was going to be about.

And, they did tell me this would work although they would not tell me what the meeting was about.

I then bought my tickets and got excited to be going to the White House.  However, fate would not be so kind to me.  My daughter got sick last week (bronchitis, and multiple spin off issues) and so I started to wonder if I really should go away.  So I tried to find out what was happening at this event.  I wrote a few friends who I knew were going and one of them told me there would be a series of talks and another told me they did not know.  So - without much other information to go on, and with a strong desire to take care of my daughter as much as possible, I cancelled my trip.

Then yesterday I got an email from a NY Times reporter

And so we connected and talked for a bit.  I found out from the phone call that the White House was announcing their Microbiome Initiative (which I knew was in the works but for which I basically knew no details).  The reporter Gardiner Harris asked me how I felt about "Big Science" types of projects and, well, I did not say nice things about them.  And I stand by those critiques of Big Science.  I talked about how I disliked the Human Microbiome Project in many ways because it fed too much money to a few groups and was prone to the same problems of other Big Science projects.  And that they were generally a waste of money.  We also discussed how I thought science worked better when administrators got out of the way and let peer review have more of a role in determining what was important.  And I said that if the new White House initiative was another top down science effort, then this would likely be a bad thing.  Or something like that.  But I did also say that I had no idea what the White House was going to announce about and I hoped it was more supportive of small science.

So the article came out and I was featured in it

Definitely something I stand by.  I think top-down approaches to science do not work well.

I woke up early this AM and started posting about the evils of Big Science.  And then I finally found an announcement with actual details on the National Microbiome Initiative being announced today.  And I was pleasantly surprised.  This was not about a big, top down approach to science.  It was more about a collection of projects under one big umbrella theme of microbiome studies.

Yes there were some top down aspects to it.  But only a component. So once I saw this, I realized my quote in the NY Times was not ideal.  Yes Big Science is bad.  But this National Microbiome Initiative is not really the standard bearer of Big Science.  It is not really even Big Science.  It is more   of a "Organizing Distributed Science".

And I found one article out there about the project that captured this essence of it:  The White House Launches the National Microbiome Initiative  by Ed Yong in the Atlantic. He nails it with this section
The National Microbiome Initiative is not the Human Genome Project—a single project with a definitive goal. It consists of many organizations operating independently; to paraphrase Whitman, it contains multitudes.
So my quote in the NY Times was technically correct - Big Science is bad.  But it also not quite right in the context it is presented - since the NMI is actually not really (or at least not completely) Big Science.  I do wish the context of the quote had been presented a bit more  (well, more specifically that I did say I did not know the full details of what they were actually proposing).  Lesson learned.  Be really careful about commenting about things "generally" without knowing the details.  I definitely regret doing that here.  I did in fact say what is reported so can't complain about being misquoted.  But I should have been more careful regarding the caveats and context.

I note - it is unclear to me how much of these smaller distributed projects would have happened without the NMI.  My guess is most of them would have happened and that the NMI is a bit of a public relations effort.  Ed Yong also captured this issue in his piece:
A cynic might be forgiven for seeing this as an exercise in branding, encapsulating what microbiome scientists were already doing under a catchy umbrella.
And I also worry as always that "Microbiomania" (hype about the microbiome) will get worse with this announcement of the NMI.  And it probably will.

But in the end I am very happy that this is not a run of the mill top down Big Science project (like the Human Genome Project or the Human Microbiome Project or the Human Brain Project).  It is much more nuanced than that.  Much more distributive.  Much more likely to support small science and creative science and such.  And that is a good thing.

True Must See TV: John Oliver on Science, Hype, and Science Reporting

This is really really really worth watching. I was pointed to it by dozens of people. And they were all right about it. Thanks people.

Also see these stories about it

Saturday, April 30, 2016

On my evolving thoughts on the #UCDavis saga involving Chancellor Linda Katehi

Still trying to wrap my brain around the controversy at UC Davis involving our Chancellor (the head of the University) Linda Katehi (see some of these news stories if you are not aware of what is going on).  In some sense I could just watch this all from the sidelines and see what happens.  But that is not in my nature.  And, over the last month I have gotten a near endless stream of comments and suggestions (some in private, some in public) about the topic.  Some say I need to be more vocal in condemning Chancellor Katehi (e.g., a student in my lab told me the other day that they have talked to faculty who are wondering why I am being so hesitant to condemn Chancellor Katehi).  Other people (many) say any negative posts about Katehi are damaging UC Davis.  Still others say and and all actions of Katehi must be considered in the context of overwhelming sexism against female leaders.  And so on.  In total I have probably gotten dozens of private comments and even more public comments about the case with suggestions for what I should be doing here.

For those who know me or know about me, I assume you know I am not exactly shy about expressing my opinions on topics like behavior of academics or academic institutions.  For example, just after joining UC Davis I wrote a post that was shared widely, condemning a UC Davis Vice Provost over her misuse of her position in support of Closed Access publishing: Vice Provost of U. C. Davis on the wrong side of Open Access.

I give out all sorts of snarky awards on my blog to friends, colleagues, and other folds in the world for doing things I think are inappropriate (e.g., see this STAT story). Sometimes I go overboard in this, but certainly I am not hesitant at expressing thoughts when I think there has been something untoward going on.  I try as much as possible to turn my microscope on myself and UC Davis too.  For example, see this post from a few weeks ago: UC Davis Storer Lecture series - since 1963 87% of speakers are male.
Again, I know I overdo this sometimes but I am certainly not hesitant to make my feelings know.

But the case of Chancellor Katehi leaves me on the fence and with my fingers unclear what to type somewhat.  And so I thought I would try to write up what my thoughts are here, even if they are muddled.  I wonder what other people think of the situation and would love feedback (as always) on this post.

So - what is so complex here?  What am I trying to wrap my brain around?  I think my challenge here comes down to the following: I don't know whether some of the responses (including mine) to Chancellor Katehi's actions are tinged with bias, especially sexism.  Or, in other words, are the actions and inactions of Chancellor Katehi "firing offenses" or have they been overblown by biased and sexist points of view.

And honestly, I do not know exactly how to figure this out.  On the one hand, I accept that there are massive amounts of sexism in society and certainly in regard to how we judge women in power.  On the other hand, I think the actions and inactions of Chancellor Katehi and her administration have been serious (in a bad way).  I note - one thing I have done to try and better understand my own feelings and actions in this saga is to compile all my posts and communications as best I can and go through them.

This has helped me sort out my thoughts and also helped show me at least that I was certainly not going easy on the UC Davis administration over these cases.  I also re-examined my posts about the Pepper Spray incident and aftermath from 2011 which has many parallels to the current situation and also involved Chancellor Katehi. See here for those: posts about the UC Davis Pepper Spray Incident and Aftermath.

Below is a discussion based in part on going through the news stories and posts of others and posts of mine.

Maybe it is best to start with this.  A few weeks ago I was pondering the fate of Chancellor Katehi and I wrote a detailed post about this The #UCDavis Chancellor's Board Positions and the Need for a More Public, Open and Early Disclosure System.

I also included in that discussion some possible conflicts of interest of my own that might be clouding my judgment.  Those are relevant to this post too and I encourage people to read them.  Anyway, this post was written at the beginning of the latest controversy when all that had been disclosed was her acceptance of a set of outside Board positions that were controversial.  I had written many mini posts and Tweets about the situation such as those below:

And I also had started to see some calls for her to be fired and such and made a point to say I did not feel things were that far along and I also linked to some of those posts.