The Tree of Life

Time 2021-11-05 10:20:31

Web Name: The Tree of Life

WebSite: http://phylogenomics.blogspot.com

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The Tree of Life

Blog of Jonathan A. Eisen, Professor at U.C. Davis.

Sunday, May 16, 2021 Some thoughts on the CDC new mask guidance

See this thread

I am with @kprather88 here. Really vexed by what @CDCDirector and @CDCgov have done here. I mean, I get the general idea of trying to return to normal and encourage vaccination. But here are some thoughts for why I am still a bit vexed. https://t.co/tTzdFYoTqU

Jonathan Eisen (@phylogenomics) May 14, 2021

Made into a thread reader thread here: https://threadreaderapp.com/thread/1393025234303741954.html

-May 16, 2021No comments: Email ThisBlogThis!Share to TwitterShare to FacebookShare to Pinterest Saturday, March 27, 2021 Compiling some of my Twitter comments about the evolution and origins of SarsCoV2/ COVID19

News Stories Quoted in

UC Davis Aggie: Emerging SARS-CoV-2 variants raise concern for the future of the pandemic9/15/2020. Newsweek.Fact-check: Does a New Study Give Evidence that the Coronavirus Was Made In a Lab?May 17, 2020. Newsweek:Scientists Shouldn't Rule Out Lab As Source of Coronavirus, New Study SaysApril 27, 2020. The controversial experiments and wuhan lab suspected of starting the coronavirus pandemic. Newsweek.
Twitter Threads

Relating to the lab vs natural origin theory of #SarsCOV2. I would like to call attention to the history of the anthrax attack investigation. Circumstantial evidence, that seemed so strong to so many people, was used to falsely accuse multiple people. https://t.co/olpDu8sKT9

Jonathan Eisen (@phylogenomics) March 27, 2021

Reading: Why the COVID lab-leak theory in Wuhan shouldn't be dismissed

By @alisonannyoung in @USATODAY . #covid19 https://t.co/u42TxLOcHe

Jonathan Eisen (@phylogenomics) March 22, 2021

This is a fascinating deep look into theories about the origins of #B117 #SARSCoV2 variant:

A lone infection may have changed the course of the pandemic https://t.co/jKNgWth63T

By @mattsreynolds1 w/ comments from @EvolveDotZoo, @LauringLab @firefoxx66 @GuptaR_lab @jcbarret

Jonathan Eisen (@phylogenomics) February 10, 2021

Worth reading / rereading - on the risks of gain of function research from 2014 from The Cambridge Working Group #covid19 #GainOfFunction https://t.co/PfTd32nNHe

Jonathan Eisen (@phylogenomics) May 19, 2020

Yes, as I told @newsweek it is theoretically possible that a Chinese lab accidentally released #SARSCoV2 https://t.co/90qFnFcKJc but preponderance of evidence so far supports all natural events and the evidence actually supporting "lab release" is shown in this pic #Covid19 pic.twitter.com/TyqAiFnQuf

Jonathan Eisen (@phylogenomics) May 3, 2020

Reading: Scientists shouldn't rule out lab as source of coronavirus, new study says https://t.co/cZIyRXczrY - personally I do not find the analysis in this new paper remotely convincing 1/n

Jonathan Eisen (@phylogenomics) May 17, 2020

-March 27, 2021No comments: Email ThisBlogThis!Share to TwitterShare to FacebookShare to Pinterest Tuesday, October 20, 2020 New article out from the Eisen Lab: Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum

SeeIsolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum

Paper based on PhD thesis work of Katie Dahlhausen and wrap up of analysis led by Laetitia Wilkins.

Full citation:

Dahlhausen KE, Jospin G, Coil DA, Eisen JA, Wilkins LGE.2020.Isolation and sequence-based characterization of a koala symbiont:Lonepinella koalarum.PeerJ8:e10177https://doi.org/10.7717/peerj.10177

Acknowledgements.We thank Céline Caseys ORCID: 0000-0003-4187-9018 for her idea to search eggNOG annotations against KEGG Class 1.11 Xenobiotics biodegradation and metabolism pathways; Chris Brown ORCID: 0000-0002-7758-6447 for his script to download assemblies in batch from GenBank; Cassandra L. Ettinger ORCID: 0000-0001-7334-403X for valuable comments on the pangenome analysis and help with revising the figures. We also thank Dr. Joseph Gillespie ORCID: 0000-0002-5447-7264, Dr. Raphael Eisenhofer ORCID: 0000-0002-3843-0749 and two anonymous reviewers for comments on the submitted manuscript. Isolate 16S Sanger sequencing was performed at the UC Davis College of Biological Sciences DNA Sequencing Facility.

-October 20, 2020No comments: Email ThisBlogThis!Share to TwitterShare to FacebookShare to Pinterest Monday, September 21, 2020 Green heron at Yolo Bypass

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Green heron at #YoloBypass today #nature #birdphotography

A post shared by Jonathan Eisen (@phylogenomics) on Sep 20, 2020 at 7:11pm PDT

-September 21, 2020No comments: Email ThisBlogThis!Share to TwitterShare to FacebookShare to Pinterest Monday, August 24, 2020 Great horned owl at #YoloBypass

Went for a walk at Yolo Bypass 8/23/2020 early in the AM and got a nice view of a Great Horned Owl. Here are some pics. -August 24, 2020No comments: Email ThisBlogThis!Share to TwitterShare to FacebookShare to Pinterest Monday, June 22, 2020 Calling on all academic institutions and organizations to stop using Facebook for any official activities #FacebookAcademicBoycott
This is long long overdue. I have been wanting to write this post for a while now and just have not gotten to it.

It has become abundantly clear that Facebook has serious issues in regard to privacy (e.g., see this), fake news, support for extremism, and lack of any moral compass. It is for these and other reasons that many individuals have quit using Facebook. In recent months one particular incredibly bad aspect of Facebook that has come more into the light is its unwillingness to limit things like hate speech, fake and dangerous, conspiracy theories, and the encouragement of violence on its platform. The egregious behavior of Facebook has led to a growing number of institutions to at least temporarily limit their connections and financial support (e.g., through Ads) of Facebook. For example see:Patagonia joins growing list of companies boycotting Facebook adswhich discusses how many companies are stopping advertising on Facebook due to "Facebooks long history of allowing racist, violent and verifiably false content to run rampant on its platform.
Given it's direct and indirect support for hate speech and hate groups, and given that many people justifiably refuse to make use of Facebook pages, and groups, it is clear that any organization that carries out functions through Facebook is both supporting Facebook's policies and excluding people who justifiably do not want to make use of Facebook. Therefore, I believe it is necessary for all academic institutions and organisms to cease and desist using Facebook for any official functions. Thus any university or academic entity (e.g, journals, societies, etc) that uses Facebook in any way for official communications and activities should stop doing so and find alternative ways to engage their communities and communicate.
I have therefore deleted the Facebook Groups I maintained for my lab, my blog, microBEnet, and the UC Davis Microbiome Special Research Program. And I implore al

l academic institutions and organizations and individuals to stop using Facebook for any official activities.
(As an aside, this is not a call to stop using Facebook for personal activities, though it seems like that would be the right thing to do too. I am planning to reduce to eliminate my personal use of Facebook too)





-June 22, 2020No comments: Email ThisBlogThis!Share to TwitterShare to FacebookShare to PinterestLabels:Facebook Saturday, June 20, 2020 Introducing "Hammerhead Man" - the superhero you did not know you needed.So I was digging through some old school papers because my daughter asked me what books they had use write reports on in high school and, well, I have a lot of my English papers from high school in a box in a closet.
And in digging through this box I found a short story I wrote for a creative writing class from freshman year in college, which was taught by Catherine Tudish.
Now, mind you, I was not in a good place when I wrote this as I was reading from the death by suicide of my father. And, possibly related to that I truly have almost no memory of writing this, other than the concept of the assignment. But I read it to my kids. And, well, I actually like it. It has a lot of issues. But I think it should be expanded on. I may just revisit this.
So - here is the official first release of "Hammerhead Man". With corrections and comments from Catherine Tudish.















-June 20, 2020No comments: Email ThisBlogThis!Share to TwitterShare to FacebookShare to Pinterest Older PostsHomeSubscribe to:Posts (Atom)Most recent postSome thoughts on the CDC new mask guidance

See this thread I am with @kprather88 here. Really vexed by what @CDCDirector and @CDCgov have done here. I mean, I get the genera...

How to stop press release spam? Post embargoed PRs. Here's one about Mayans using tobacco. Just got this press release by email. I am sick of receiving dozens of unsolicited press releases, especially those in topics not related ...New article out from the Eisen Lab: Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarumSee Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum Paper based on PhD thesis work of Katie Dahlha...Thanks Google Scholar Updates for new article to read .. wish you had an #openaccess only settingI have a new friend in Google Scholar Updates I have written about the Updates system before and if you want more information please see...Search This BlogPagesHomeSTEM DiversityMicrobiomaniaTwisted Tree of Life AwardsFreeing Fathers PubsStory Behind the PaperAbout MeJonathan EisenView my complete profileBlog Archive 2021(2) May(1)Some thoughts on the CDC new mask guidance March(1) 2020(29) October(1) September(1) August(1) June(3) April(5) March(4) February(2) January(12) 2019(36) December(3) November(3) October(6) September(1) August(2) July(6) June(1) May(1) April(1) March(7) February(3) January(2) 2018(19) December(1) November(2) October(3) September(1) May(1) April(2) March(6) February(2) January(1) 2017(54) December(11) November(6) October(7) September(2) August(5) July(5) June(5) May(3) April(1) March(4) February(3) January(2) 2016(52) October(6) September(6) August(1) July(7) May(3) April(8) March(9) February(4) January(8) 2015(108) December(14) November(12) October(9) September(4) August(3) July(9) June(8) May(10) April(4) March(14) February(8) January(13) 2014(180) December(9) November(9) October(15) September(17) August(17) July(5) June(6) May(20) April(13) March(17) February(24) January(28) 2013(201) December(8) November(9) October(16) September(14) August(17) July(16) June(14) May(22) April(14) March(20) February(26) January(25) 2012(408) December(22) November(23) October(11) September(26) August(41) July(33) June(26) May(28) April(34) March(43) February(46) January(75) 2011(389) December(62) November(119) October(38) September(39) August(20) July(8) June(32) May(14) April(17) March(11) February(19) January(10) 2010(151) December(2) November(8) October(8) September(13) August(21) July(16) June(10) May(5) April(13) March(18) February(16) January(21) 2009(228) December(17) November(21) October(21) September(21) August(20) July(11) June(14) May(29) April(23) March(18) February(19) January(14) 2008(280) December(11) November(23) October(32) September(36) August(19) July(22) June(40) May(25) April(27) March(11) February(21) January(13) 2007(178) December(11) November(16) October(22) September(15) August(17) July(14) June(15) May(15) April(14) March(17) February(12) January(10) 2006(76) December(16) November(12) October(11) September(11) August(12) July(5) June(9) 2005(1) February(1)Follow @TwitterDevSubscribe ToPosts Atom PostsAll Comments Atom All CommentsmicroBEnetLoading...Eisen Lab BlogLoading...More About MeMy lab pageTalks and PresentationsPublicationsPress CoverageLinkedInmicroBEnetMy Ted TalkMe on TwitterRecent Things I Have Added to iNaturalist View phylogenomics's observations Subscribe ToPosts Atom PostsAll Comments Atom All CommentsDeep Microbial Thoughts
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by The Tree of Life: All Microbes, All the Time Popular PostsHow to stop press release spam? Post embargoed PRs. Here's one about Mayans using tobacco.Thanks Google Scholar Updates for new article to read .. wish you had an #openaccess only settingQ-Bio conference in Hawaii, bring your surfboard & your Y chromosome b/c they don't take a XXNew article out from the Eisen Lab: Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarumTurning down an endowed lectureship because their gender ratio is too skewed towards males #WomenInSTEMScience Magazine publishes "opinion" piece targeting a specific student w/ sexist "critique" and then won't publicly discuss what happened or what they will do about itTen simple ways to share PDFs of your papers #PDFtributeAAAS - Blocking Access to the Scientific Literature Even When They Say It Is "Free"A day to think, to pause, to ponderToday's misleading overselling the #microbiome - U. Chicago on Alzheimer's and gut microbes

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