The "Ben Franklin Award for Open Access in the Life Sciences" should be renamed as a "#Manward"
Uggh.So in 2011 I won this award called the "Benjamin Franklin Award for Open Access in the Life Sciences. " I was happy about it at the time. I got a book and a plaque and was toasted at a meeting in Boston. A few years ago I and others noted that the award had been given only to men. Then Helen Berman won the award in 2014 and it looked like maybe the process was starting to not be so biased.But I got alerted to the ongoing issues again by an email a few days ago. And not only have the other winners all been men, all four nominees this year are men too.Past Winners2002 – Michael B. Eisen2003 ...
Source: The Tree of Life - March 14, 2019 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs

Stalking the wild garganey in West Sacramento #birding #eBird #iNaturalist #birdphotography #nikonD500
So - I did a thing today. A new thing for me. I officially became a bird nut. For the first time in my life, I went on an outing to see a rare bird that I read about online.I went to West Sacramento, to a pond there, to see, and hopefully take pictures of, a garganey. What, you ask, is a garganey? It is a kind of duck. According to Wikipedia:The garganey (Spatula querquedula) is a small dabbling duck. It breeds in much of Europe and western Asia, but is strictly migratory, with the entire population moving to southern Africa, India (in particular Santragachi), Banglade...
Source: The Tree of Life - March 9, 2019 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs

Kisaco Research - sponsoring YAMMMM - yet another mostly male microbiome meeting - again - not their first biased rodeo
Well, sadly, I am not shocked by this. Disappointed, yes. But not shocked. Just got an announcement sent to me for this meeting: Animal Microbiome USA 2019 | Kisaco ResearchHappening next week in Kansas City. Run by Kisaco Research. I have written about their propensity to have meetings where most of the speakers were white men previously. SeeAnother white men's microbiome meeting from Kisaco #YAMMM #manel #STEMDiversityThe White Men's Microbiome Congress #YAMMM #Manel #BoycottPeople from the company claimed they were going to do better in the future. And maybe they have for some meetings...
Source: The Tree of Life - March 6, 2019 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs

If a body wash falls in the forest, is it gentle on the microbiome?
Well, I guess I am happy Dove is interested in the microbiome. My exposure to Dove's thinking on the microbiome started with an ad that was shared with me by Christine Parks.The ad claims that Dove is gentle on the microbiome. OK. I am not sure I get what that means completely. But I think they are saying "Our product does not mess up your microbiome". I guess this could be good for some people if it were true. But for others, maybe you want to mess up the microbiome. Regardless, I would love to see data, if it exists, behind such a claim because my guess is that any body wash affects up the m...
Source: The Tree of Life - March 4, 2019 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs

Interesting and important story on fecal transplants in @nytimes
This is definitely worth a read:Drug Companies and Doctors Battle Over the Future of Fecal Transplants - The New York Times. By Andrew Jacobs. March 3, 2019.The lead in is good:CAMBRIDGE, Mass. — There’s a new war raging in health care, with hundreds of millions of dollars at stake and thousands of lives in the balance. The battle, pitting drug companies against doctors and patient advocates, is being fought over the unlikeliest of substances: human excrement.The story is both interesting and includes some very important stuff going on behind the scenes that may affect the future of fecal transplants as a treatment in ...
Source: The Tree of Life - March 4, 2019 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs

A conference where all the speakers are women - happening this week #YAMMM #manels #STEMDiversity #GenderBias
It was now six years ago that I wrote here wondering if it would be a good idea to have a conference where all the speakers were women.See The Tree of Life: A conference where the speakers are all women?I wrote about this because of the general issue with excessive numbers of conferences where most or all of the speakers were men. I had come up with a term for such meetings -YAMMM. Yet Another Mostly Male Meeting. I even made some little pics / images to represent such YAMMMs.And I blogged and Tweeted about such meetings a lot (and still do). See STEM Diversity posts and related links her...
Source: The Tree of Life - February 26, 2019 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs

Today's microbial diversity reading: A census-based estimate of Earth's bacterial and archaeal diversity
Looking at this today:A census-based estimate of Earth's bacterial and archaeal diversityLouca S, Mazel F, Doebeli M, Parfrey LW (2019) A census-based estimate of Earth's bacterial and archaeal diversity. PLoS Biol 17(2): e3000106. https://doi.org/10.1371/journal.pbio.3000106Definitely worth a look:AbstractThe global diversity of Bacteria and Archaea, the most ancient and most widespread forms of life on Earth, is a subject of intense controversy. This controversy stems largely from the fact that existing estimates are entirely based on theoretical models or extrapolations from small and biased data sets. Here, in an attem...
Source: The Tree of Life - February 9, 2019 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs

Symbiosis paper of interest: Host-Microbe Coevolution and Complex Marine Invertebrate Holobionts | mBio
This looks potentially interesting.Host-Microbe Coevolution: Applying Evidence from Model Systems to Complex Marine Invertebrate Holobionts | mBioO ’Brien PA, Webster NS, Miller DJ, Bourne DG. 2019. Host-microbe coevolution: applying evidence from model systems to complex marine invertebrate holobionts. mBio 10:e02241-18.https://doi.org/10.1128/mBio.02241-18.ABSTRACTMarine invertebrates often host diverse microbial communities, making it difficult to identify important symbionts and to understand how these communities are structured. This complexity has also made it challenging to assign microbial functions and to unrave...
Source: The Tree of Life - February 9, 2019 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs

Wakelet of UC Davis "Research Quality and Design Symposium"
Made a mini Wakelet: -------- This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter. -------- (Source: The Tree of Life)
Source: The Tree of Life - January 29, 2019 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs

And today in the Twisted Tree of Life Award - the only way to study evolution is to try and make fake reconstructions of past events
This article basically discounts all evolutionary analysis and ends with this inane and totally BS line about this artificial reconstruction"Next to having been there, this is as good as it gets" 4/n— Jonathan Eisen (@phylogenomics)January 10, 2019 -------- This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter. -------- (Source: The Tree of Life)
Source: The Tree of Life - January 9, 2019 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs

Twisted Tree of Life Award: University of Nebraska Lincoln Press Release on Archaeal Epigenetics
Well this one is really painful. So painful I am re-starting my "Twisted Tree of Life" Award posts here.See Tweets about it below:A lot of pretty painful evolution babble in this press release about archaea epigenetic: Evolution sans mutation discovered in single-celled archaeahttps://t.co/aumbdfhU4R#TwistedTreeOfLife— Jonathan Eisen (@phylogenomics)December 10, 2018For example - there is a claim that this might have something to do with why archaea don't produce antibiotics which would at best be an evolution just so story except for the part where archaea do produce antibiotics (eg Halocins)— Jonathan Eisen (@ph...
Source: The Tree of Life - December 10, 2018 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs

YAMMMM: Yet Another Mostly Male Microbiome Meeting - Gut Microbiota for Health World Summit 2019
Uggh. In the middle of a faculty retreat and saw a Tweetabout this meetingand could not help looking at their speaker list. And am not impressed. Too many male speakers.Gut Microbiota for Health World Summit 2019A Meeting to HearMen (81%) NotWomen (19%) Discussing Microbiota*, **YAMMMM: Yet Another MostlyMale Microbiome MeetingGail A. Hecht, MD, MS, Loyola University Medical Center (U.S.)Jack A. Gilbert, PhD, University of Chicago (U.S.)Session Moderator:Giovanni Barbara, MD, University of Bologna (Italy)Suzanne Devkota, PhD, Cedars-Sinai Medical Center (U.S.)Magnus Simren, MD, PhD, AGAF, University of Gothenburg...
Source: The Tree of Life - November 29, 2018 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs

Pumpkin Carving as a model for Genome Assembly
So - we have this pumpkin carving contest every year in the UC Davis Genome Center. And people from my lab have done some excellent pumpkins in the past.See for example some details on their 2014 pumpkin:The@phylogenomics lab pumpkin started out simple:@casettron@hhollandmoritz (1/2)pic.twitter.com/gZJNMqPzaf— David Coil (@davidacoil)October 29, 2014And thus, the@phylogenomics lab annual pumpkin was created. You have to look through the objectives to see it.pic.twitter.com/G3t5Iyo6gL— Russell Neches (@ryneches)October 29, 2014The pumpkin entry from@phylogenomics's lab is a little unusual!pic.twitter.com/4sNslv9x8x...
Source: The Tree of Life - November 3, 2018 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs

And today in #microbiomania (aka overselling the microbiome) - ridiculous claim from Raphael Kellman's book marketing group
Just got this email below. It is from a marketing person promoting Raphael Kellman's new book. And it has an absolutely dangerous, ridiculous claim in it. They claim that if you have memory loss, or mood problems, these are not in your head at all - this is caused my problems in your microbiome. What absolutely bullshit. Sure, the microbiome can impact the brain and mood. But to go from that to claiming that all memory loss and mood issues are due to problems with the microbiome. Dangerous. Deceptive. Scary. Snake oil.But yes, I would be happy to write about your book. Righ...
Source: The Tree of Life - October 31, 2018 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs

Some Deep Microbial Thoughts T Shirts
Someone asked me about these T-shirts yesterday and I had forgotten about them. I had to contact Zazzle to figure out how to get back into the account. And I figured I would post a few links to them here. You can also see them at Zazzle here: Tree of Life StoreMulti-cellular eukaryocentrismbyjonathaneisenCasablanca symbiosisbyjonathaneisenMutualism love storybyjonathaneisenMay the microbes be ever in your favorbyjonathaneisenI have always depended on the kindness of microbesbyjonathaneisenThe greatest trick a pathogen ever pulled was convbyjonathaneisenWe will always have parasitesbyjonathaneisenI love ...
Source: The Tree of Life - October 29, 2018 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs