Wednesday, April 30, 2014

Grant review: Eisen may not be able to help much due to time spent on blog; Eisen's response - blog about it

Wrote a draft of this post in 2012.  Decided to post it now since I included some information about it in a talk and it has gotten some reaction on the intertubes (e.g., Blog about science? Kiss your grant proposal goodbye).  This is what I wrote after getting the reviews back and decided, for various reasons, to never post.  In retrospect, I think I should have posted then ...

Got this back in a grant review for a project that I have a minor role in:
Outstanding group of individuals, and the organizational and management structure appears sound with clear roles and responsibilities of theme faculty. There is a large focus on developing this for microbiome research, but Eisen seems to be the only team member with this expertise, and may not have the bandwidth to coordinate this on such a large project alone, especially given his high time commitment to his blog
I started drafting a letter to the reviewer - partly about how great I think I am and partly to vent some anger ... here is the beginning:
Dear Reviewer 
  1. Fuck you.
  2. Apparently getting elected to the American Academy of Microbiology this year was due to my blogging.
  3. I have 31907 citations in Google Scholar.  What the fuck do you have?
  4. My blog is in fact about EXACTLY what we were talking about in the proposal, you fucking piece of fucking shit.
  5. Fuck you.
  6. You are right in a way - I have little time to spare.  Did I somehow not do something you wanted me to do?  Fine.  Say that.  But focusing on my blog just shows you are a ...
But then I realized this was a bit too much.  I should not let this comment lead me to get defensive about my career, my blog, etc.  Plus, I was spending too much time on this.  (The above took 2 minutes and 12 seconds to write and then another 1 minute and 11 seconds to highlight and link up and ponder).  So I decided to be more concise
Dear Reviewer 
Fuck you. 
Jonathan Eisen
But then I realized,  cursing was not the solution.  Maybe love would be better?

Dear Reviewer 
Thank you for your insight.  I will do my best to spend less time blogging in the future.
Jonathan Eisen
But this still did not seem right.  So I decided that the best option was to do nothing.  So that is what I am doing.  Nothing.  No response.  No blog post.  Nothing.  There.  I feel better already.

NSF asks for comments on "genomes-phenomes" program; here's a comment - phenome is a silly #badomics term

Hmm.  Just got this in the emails.
BIO seeks community input on Genomes-Phenomes research frontiersJohn Wingfield, Assistant Director of the National Science Foundation Directorate for Biological Sciences (BIO), is pleased to announce the posting of a Wiki to seek community input on the grand challenge of understanding the complex relationship between genomes and phenomes.  The Wiki is intended to facilitate discussion among researchers in diverse disciplines that intersect with biology, such as computation, mathematics, engineering, physics, and chemistry.The Wiki format encourages open communication, captures new viewpoints, and promotes free exchange of ideas about the bottlenecks that impede progress on the genomes-phenomes grand challenge and approaches or strategies to overcome these challenges. Information provided through the Wiki will help inform BIO's future research investments and activities relevant to understanding genomes-phenomes relationships.To provide comments, ask questions and view input from and interact with other community members, first-time users should sign up for an account via this link:Sign-up.  Once registered, users will be directed to the main page of the NSF Wiki to accept the terms and conditions before proceeding.  Additional guidance and subsequent visits can be accessed via this link: Genomes-Phenomes Wiki.Community members should feel free to forward notice of this to anyone they think might be interested in contributing to the discussion. Questions regarding the Wiki should be sent to

Nice that they are seeking input. But really - does NSF have to adopt "phenome" as a term? How exactly is this different from "phenotype"? This seems to be a case of exactly what I was criticizing in my Badomics article in Gigascience and in all my posts here (eg bad omics words of the day, Worst New Omics Word Award, badomics, etc). Blech. Genomics is really interesting. I have worked on it for many years. But there is no need to contaminate the literature by using new, uninformative, oversold terms like "phenome".

Sunday, April 27, 2014

Overselling the microbiome award: Mercola/Perlmutter on fecal transplants for severe neurological dysfunction

Well, this is pretty scary.

An automated Google Search I have picked up a hit to an article by Mercola about an interview he did with David Perlmutter: Key Dietary Strategies to Protect Yourself from Alzheimer’s : Natural Wellness Review

And the article covers many topics but one is pretty over the top.  There is a section on recommendations by Dr. Perlmutter to promote brain health.  And one of them is quoted below:
Fecal transplantation, in cases of severe neurological dysfunction where poor gut flora appears to be a contributing factor. Your microbiome is critical for multiple reasons, including regulating the set point of inflammation, producing neurotransmitters like serotonin, and modulating systems associated with brain function and brain health. This form of therapy is now the standard of care for life-threatening C. difficile infections.
Yup.  He is recommending fecla transplants to treat severe neurological dysfunction.  Not the first person to suggest a connection between microbes and neurology.  Not the first person to say that maybe trying to change the microbiome might be an interesting thing to test as a treatment for some issues.  But with no caveats here they just jump right in to using this to treat neurological dysfunction.  This is just grossly over the top and will likely mislead many many people with neurological dysfunctions into thinking fecal transplants are a known effective treatment.  I wonder if Dr. Perlmutter will start offerring home fecal transplant kits for sale on his web site (which I will not link to here).

Now, I think microbes are important.  And I think there is potential here for fecal transplants for a lot of issues.  But potential is different than proven.  By a long show.  And people like Mercola and Dr. Perlmutter should be ashamed for misleading people like this.  And thus they are today's winners of an "Overselling the Microbiome" award.

Storify roundup of links & pics about evolution, microbes, open science, etc

So I just don't have time to do a compilation of links with extra detail about them like some people do regarding interesting information and stories they have seen over the last week or so. Instead I am trying to compile such information via Twitter posts of mine and then converting the more relevnt ones into a Storify. So here is one such storification for the last month or so.

Friday, April 25, 2014

Today's wondering - why are so few of the speakers at "UC Drought Summit" women?

Got pointed to YAMWASGR (yet another meeting with a skewed gender ratio) this AM via Twitter.

This was in reference to a meeting in Sacramento:  Apr. 25: UC Drought Summit, free and open to public | Center for Watershed Sciences and alas the gender ratio is definitely skewed on the speaker list.  Men in Blue, Women in Yellow.
  • UC activities to reduce water use on and off campus
    • • Barbara Allen-Diaz, UC Division of Agriculture and Natural Resources 
    • • Matthew St.Clair, University Office of the President
  • Current drought: causes, how bad is it, and will we see more like it?
    • • Amir AghaKouchak, UC Irvine
    • • Michael Anderson, State Climatologist
    • • Daniel Cayan, UC San Diego
    • • William Collins, UC Berkeley; Intergovernmental Panel on Climate Change
    • • Glen MacDonald, UCLA
    • • Daniel Swain, Stanford University
  • Drought-proofing California?
    • • Michael Stenstrom, UCLA 
    • • Jay Lund, UC Davis
  • Kenneth Baerenklau, UC Riverside
    • Roger Bales, UC Merced
    • • Charles Burt, Cal Poly San Luis Obispo
    • • Frank Loge, UC Davis
    • • Stephanie Pincetl,UCLA
    • • Scott Stephens, UC Berkeley
  • Remarks by Chancellor Linda P.B. Katehi, UC Davis
  • Economic consequences of the drought: agriculture, energy, forests, industry and water
    • • Katrina Jessoe, UC Davis
    • • Anthony Madrigal, Twenty-Nine Palms Band of Mission Indians 
    • • Josué Medellín-Azuara, UC Davis
    • • Daniel Sumner, UC Agricultural Issues Center
    • • David Sunding, UC Berkeley
  • Endangered species and drought: science, management and policies
    • • Richard Frank, UC Davis
    • • Ellen Hanak, Public Policy Institute of California
    • • David Hayes, Stanford University; former deputy Interior secretary
    •  • Peter Moyle, UC Davis
    • • David Sedlak, UC Berkeley
    • • Joshua Viers, UC Merced
  • State policy for future droughts: groundwater, storage, marketing and conservation
    • • Jay Famiglietti, UC Irvine
    • • Thomas Harter, UC Davis
    • • Ruth Langridge, UC Santa Cruz
    • • Steve Macaulay, consultant
    • • Samuel Sandoval Solis, UC Davis 
    • • Kurt Schwabe, UC Riversidepage2image9504     page2image9928
That comes out to 26:6 in my count or 18.8% female, 81.2% male.  Now, I note - I have no idea what the "pool" looks like in this area, but such a % certainly does not look good from an outside (to the field, even though I am an insider in that this was organized by some people at UC Davis).   Once again, I would like to point out to meeting organizers, that having a diverse pool of speakers for a meeting is important for many reasons and sometimes it takes extra work to pull it off, but in my experience it is definitely worth it.

Tuesday, April 22, 2014

A special special issue of RNA Biology - dedicated to Carl Woese and Open Access too

A must read for, well, everyone out there: RNA Biology: Table of Contents for a special issue dedicated to / about Carl Woese.  The issue includes an amazing collection of papers:

A special issue in memoriam of Carl Woese
Renée Schroeder
Page 169

Introduction to special Carl Woese issue in RNA Biology
Robin R Gutell
Pages 170 - 171

Carl Woese: A structural biologist’s perspective
Peter B Moore
Pages 172 - 174

Early days with Carl
Ralph Wolfe
Page 175

Molecular phylogenetics before sequences: Oligonucleotide catalogs as k-mer spectra
Mark A Ragan, Guillaume Bernard and Cheong Xin Chan
Pages 176 - 185

Constraint and opportunity in genome innovation
James A Shapiro
Pages 186 - 196

Carl Woese's vision of cellular evolution and the domains of life
Eugene V Koonin
Pages 197 - 204

From Woese to Wired: The unexpected payoffs of basic research
Ann Reid
Pages 205 - 206

Carl Woese, Dick Young, and the roots of astrobiology
John D Rummel
Pages 207 - 209

Life is translation
Bojan Zagrovic
Pages 210 - 212

Organelle evolution, fragmented rRNAs, and Carl
Michael W Gray
Pages 213 - 216

Remembering Carl Woese
Kenneth R Luehrsen
Pages 217 - 219

Woese on the received view of evolution
Sahotra Sarkar
Pages 220 - 224

This article is open accessSecondary structure adventures with Carl Woese
Harry F Noller
Pages 225 - 231

A backward view from 16S rRNA to archaea to the universal tree of life to progenotes: Reminiscences of Carl Woese
Roger A Garrett
Pages 232 - 235

Carl Woese in Schenectady: The forgotten years
Larry Gold
Pages 236 - 238

History and impact of RDP: A legacy from Carl Woese to microbiology
James R Cole and James M Tiedje
Pages 239 - 243

Casting a long shadow in the classroom: An educator’s perspective of the contributions of Carl Woese
Mark Martin
Pages 244 - 247

Looking in the right direction: Carl Woese and evolutionary biology
Nigel Goldenfeld
Pages 248 - 253

Ten lessons with Carl Woese about RNA and comparative analysis
Robin R Gutell
Pages 254 - 272

Memories of Carl from an improbable friend
Harris A Lewin
Pages 273 - 278