Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

Collecting links to blogs that focus entirely or partly on microbiology topics #ASM2012

Making a list of blogs that focus entirely or partly on microbiology topics.  Here are some.  Would love suggestions for others. Obviously not all are of equal quality in terms of the writing or the science but the diversity is impressive.

  1. Aetiology from Tara Smith scienceblogs.com/aetiology
  2. A Flu Diary http://afludiary.blogspot.com/
  3. AIDS.GOV blog.aids.gov/
  4. Antibiotics: the perfect storm from David Shlaes antibiotics-theperfectstorm.blogspot.com/
  5. Antimicrobial Resistance from Miriam Barlow antimicrobial.blogspot.com
  6. Aspergillus Website Blog aspergillusblog.blogspot.com/
  7. Avian Flu Diary afludiary.blogspot.com/
  8. BacterioFiles from Jesse Noar bacteriofiles.blogspot.com
  9. Bacpathogenomics bacpathgenomics.wordpress.com/
  10. Bacteriophage, microbiology and the battle for funding from Philip Skipper phageresearch.blogs.lincoln.ac.uk/
  11. BioBE center Blog: biobe.uoregon.edu/
  12. Blastocystis Blog: blastocystisblog.blogspot.com/
  13. Barf Blog barfblog.foodsafety.ksu.edu/barfblog 
  14. Chimeras chimerasthebooks.blogspot.com/
  15. CoastalPathogens coastalpathogens.wordpress.com/
  16. Contagions from Michelle Ziegler contagions.wordpress.com
  17. Controversies in Hospital Infection Prevention haicontroversies.blogspot.com/
  18. Creepy Deadly Wonderful Parasites parasitewonders.blogspot.com/
  19. Curiosidades de la Microbiología curiosidadesdelamicrobiologia.bl…
  20. Cyanobacterial Adventures cyanobacterialadventures.blogspot.com/
  21. Daily Parasite dailyparasite.blogspot.com/
  22. Daniel Wilson’s Blog blog.danielwilson.me.uk/
  23. Dawn in Antarctica dawninantarctica.blogspot.com/
  24. El buit del temps blocs.mesvilaweb.cat/bloc/view/id/5664
  25. End the Neglect endtheneglect.org/
  26. Epidemonomics www.cddep.org/blog
  27. ERV from Abbie Smith scienceblogs.com/erv/
  28. Food Poison Journal www.foodpoisonjournal.com/
  29. Food Safety and Environmental Health blog www.safefoodsblog.com/
  30. Foraminifera Blog foraminifer.blogspot.com/
  31. Fun with Microbiology (What’s Buggin’ You?) http://thunderhouse4-yuri.blogspot.com/
  32. History of Vaccines www.historyofvaccines.org/blog
  33. HIV This Week http://hivthisweek.unaids.org/
  34. Hospital Infection Control and Prevention hicprevent.blogs.ahcmedia.com/
  35. Human Microbiome Journal Club hmjournalclub.wordpress.com/
  36. Indian Initiative for Management of Antibiotic Resistance save-antibiotics.blogspot.com/
  37. Infection Landscapes infectionlandscapes.org
  38. Infectious Diseases Today bactiman63.blogspot.com/
  39. International AIDS Vaccine Initiative www.iavireport.org/IRblog/default.aspx 
  40. It’s a small world fuckyeahmicrobiology.tumblr.com/
  41. Jason Tetro at the Huffington Post www.huffingtonpost.ca/jason-tetro/ *
  42. JHU Phage Hunters jhuphagehunters.wordpress.com/
  43. Lab Rat blogs.scientificamerican.com/lab…
  44. mBIO mbioblog.asm.org/mbiosphere
  45. Malaria World malariaworld.org/blog
  46. Matryoshka from Jeff Smith matryoshka.org/
  47. Memory Reactivation memoryreactivation.wordpress.com/
  48. Memoirs of a Defective Brain defectivebrain.fieldofscience.com/
  49. microbelog microbelog.wordpress.com/
  50. MicroBichitos blogs.elpais.com/microbichitos
  51. Microbial Diversity from Irene Newton microdiv.blogspot.com/
  52. microBEnet blog from Jonathan Eisen, David Coil, Holly Bik www.microbe.net/microbenet-blog/ 
  53. Microbe Matters from KD Shives http://kdshives.com
  54. Microbiology Bytes from AJ Cann microbiologybytes.com/blog
  55. Microblogology from Lorraine Cramer  microblogology.com/
  56. Microbiology Stories bacteriastories.blogspot.com/
  57. Mike the Mad Biologist mikethemadbiologist.com/
  58. Miss Parasitos missparasitos.blogspot.com/  AND missparasitesinenglish.blogspot.com/
  59. Monotreme’s Blog monotreme1000.wordpress.com/ *
  60. MyChrobial Romance from David Baltrus mychrobialromance.blogspot.com/
  61. Mycorant mycorant.com
  62. MycorWeb Fungal Genomics mycor.nancy.inra.fr/blogGenomes
  63. Mystery Rays from Outer Space www.iayork.com/MysteryRays/
  64. Not Exactly Rocket Science from Ed Yong blogs.discovermagazine.com/notrocketscience/
  65. Of Bacteria and Men from Robin Tecon ofbacteriaandmen.blogspot.com/
  66. One in Seven People http://oneinsevenpeople.co.uk/
  67. Outbreak News outbreaknews.com/
  68. Parasite of the Day dailyparasite.blogspot.com/
  69. Parasites http://www.rosemarydrisdelle.com/
  70. Pathogens, Genes and Genomes pathogenomics.bham.ac.uk/blog
  71. Pharmaceutical Microbiology by Tim Sandle pharmig.blogspot.com/
  72. Public Health Matters from the CDC blogs.cdc.gov/publichealthmatters/
  73. Rapid Microbiology Methods rapidmicromethods.com/ 
  74. RRResearch from Rosie Redfield rrresearch.blogspot.com
  75. Rule of 6ix from Connor Bamford ruleof6ix.fieldofscience.com
  76. Russell’s Blog from Russell Neches vort.org/
  77. Safe Food from John Brooks foodsafetywithjaybee.blogspot.com/
  78. Skeptic Wonder skepticwonder.fieldofscience.com
  79. Skewed Distribution skeweddistribution.com/
  80. Small Things Considered schaechter.asmblog.org/schaechter
  81. Smaller Questions www.smallerquestions.org/
  82. Sociobiology sociobiology.wordpress.com/
  83. Spirochetes Unwound spirochetesunwound.blogspot.com
  84. Superbug wired.com/wiredscience/superbug
  85. Superbugs and Drugs superbugsanddrugs.blogspot.com/
  86. Stringent Response stringentresponse.blogspot.com/
  87. Symbionticism from Seth Bordenstein symbionticism.blogspot.com/
  88. The Artful Amoeba blogs.scientificamerican.com/art…
  89. The Febrile Muse febrilemuse-infectious-disease.blogspot.com/
  90. The Genome Factory thegenomefactory.blogspot.com/
  91. The “Germ Guy” Blog: germguy.wordpress.com/
  92. The Hyphal Tip by Jason Stajich fungalgenomes.org/blog
  93. The Intestinal Gardner intestinalgardener.blogspot.com/
  94. The Loom from Carl Zimmer blogs.discovermagazine.com/loom
  95. The Oceloid from PSI Wavefunction blogs.scientificamerican.com/oceloid
  96. The Parasite Diary parasitediary.wordpress.com/
  97. The Tree of Life from Jonathan Eisen phylogenomics.blogspot.com
  98. Ultraphyte from Joan Slonczewski ultraphyte.com/
  99. We Beasties from Kevin Bonham scienceblogs.com/webeasties/
  100. The View from a Microbiologist from Samantha Price theviewfromamicrobiologist.fieldofscience.com/
  101. Viroblogy from Ed Rybicki http://rybicki.wordpress.com/
  102. Virology Blog from Vincent Racaniello virology.ws
  103. Viral Bioinformatics from Chris Upton athena.bioc.uvic.ca/blog/
  104. Worms and Germs www.wormsandgermsblog.com/
  105. Zoonotica zoonotica.wordpress.com
Podcasts and Videocasts


Not screened yet but considering adding to the above list

To add to list

Other stuff about microbes but not quite bloggy enough for my list above

Microbiology related blogs that are appear to be no longer active or very rarely active

Twitter lists
Paper.lis
Scoop.It
Science Blogs Networks that might have some microbial content not listed above
——–
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.

——–

Coming up at the #ASM2012 mtg. "The Great Indoors: Recent Advances in the Ecology of Built Environments"

The American Society for Microbiology meeting is starting tomorrow and there are multiple things related to microbiology of the built environment there.  These include a session that was organized by Brendan Bohannan which I am chairing.

The details of the session are below:

Session Title: The Great Indoors: Recent Advances in the Ecology of Built Environments

Session Date/Time: Sunday Jun 17, 2012 3:00 PM – 5:30 PM

Session Room: Esplanade Ballroom 300

Description: Although humans in industrialized countries spend nearly 90% of their time in enclosed buildings, we know very little about the biology of the indoor environment. However, this is starting to change. Over the past few years, the field of indoor ecology has grown dramatically. Ecologists are beginning to apply ecological theory and concepts to understanding buildings as ecosystems. A new understanding of the biodiversity of built environments is emerging, as well as a new appreciation of the importance of interactions between humans and non-human life indoors. The proposed symposium will showcase this emerging understanding. We will feature presentations that demonstrate the utility of ecological theory for understanding built environments, that describe the dynamics of biodiversity indoors and that illustrate the interactions of humans with indoor ecology. Our focus will be on the ecology of the dominant forms of non-human life indoors – microorganisms – and their interactions with humans.

 Talks

  • Jonathan Eisen microBEnet: the microbiology of the built environment network
  • Nicholas Be: Examination of the environmental air microbiome using deep sequencing
  • Katie Kirsch: A microbial analysis of environmental surfaces in hotel rooms
  • Mark Hernandez: Stability of airborne microbes to master environmental variables
  • John Senko: Microbial communities associated with flue gas desulfurization systems
  • Kimberly Ross: Drinking water delivery networks as microbial ecosystems
  • Jordan Peccia: The effect of environmental conditions on the allergenic potency of Aspergillus fumigatus spores
——–
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.

——–

The human #microbiome project (HMP): new papers and news stories

Just collecting here the new papers from the Human Microbiome Project and some news stories discussing them.

Main papers in Nature

PLoS Collection (all free)

Other paper out in Nature on the topic though not from the HMP

Some news stories:

Some previous posts of mine in this general area

Some other good recent posts or articles worth looking at on the topic
Related links
And of course – a gratuitous embed of my recent TEDMED talk
——–
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.

——–

Pics from the Redrum hotel in DC where we stayed for #SAMG12

Img_3376 Img_3369

Img_3357

See the full gallery on Posterous

IMG_3368.MOV Watch on Posterous

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——–
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.

——–

Pics from the Redrum hotel in DC where we stayed for #SAMG12

 

Img_3376 Img_3369 Img_3357

See the full gallery on Posterous

IMG_3368.MOV Watch on Posterous

IMG_3362.MOV Watch on Posterous

IMG_3370.MOV Watch on Posterous

IMG_3377.MOV Watch on Posterous

IMG_3371.MOV Watch on Posterous

——–
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.

——–

At IOM Forum on Microbial Threats "Science And Applications of Microbial Genomics" #SAMG12

At IOM Forum on Microbial Threats “Science And Applications of Microbial Genomics” meeting in DC. To find out current details on the meeting check out Twitter hashtag #SAMG12. See feed below (though it is easier to go to Twitter to follow #SAMG12).
http://widgets.twimg.com/j/2/widget.jsnew TWTR.Widget({ version: 2, type: ‘search’, search: ‘#SAMG12’, interval: 30000, title: ‘IOM Meeting on “Science and Applications of Microbial Genomics”‘, subject: ‘All microbes, all the time’, width: 500, height: 1000, theme: { shell: { background: ‘#8ec1da’, color: ‘#ffffff’ }, tweets: { background: ‘#ffffff’, color: ‘#444444’, links: ‘#1985b5’ } }, features: { scrollbar: false, loop: false, live: true, behavior: ‘all’ } }).render().start();

——–
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.

——–

Updates on the #UCDavis Academic Freedom situation

A few days ago I wrote a post: Report on “Egregious Academic Freedom Violation” at #UCDavis.  The post provides some detail on an investigation carried out by the UC Davis Academic Senate into a case of apparent retribution at the UC Davis medical school.  In the case the Dean of the Medical School (Claire Pomeroy), the Executive Associate Dean Fred Meyers and the Health System Counsel appear to have carried out a retribution of sorts against a member of the faculty at the medical school (NOTE – I have a half appointment at the medical school).  The faculty member – Michael Wilkes had the gall to write an editorial (with Jerome Hoffman) for the SF Chronicle expressing opinions about a medical issue and actions of some people at the UC Davis Medical School.  Apparently, some people at the medical school did not like being criticized.  The result?  A threat to take away his space, to remove him as instructor of a medical school course, and other incites including a threatening email/letter from the medical school counsel.  Lovely.

Fortunately, the UC Davis Academic Senate was brought into the case by Wilkes and a committee of the academic senate responded VERY strongly with a report (see my previous post with more detail).  Meanwhile – news of the report spread and was covered in Inside Higher Ed.  It was then that I heard about it and felt the need to blog about it.  And news has spread a bit more (thank you PZ Myers and others).  On Friday, the UC Davis Academic Senate met (and though I am not a member of the Senate, I went to the meeting).  And the Senate passed three resolutions coming out strongly in support of Prof. Wilkes and critiquing the behavior of the Dean, Asst. Dean and Counsel from the Med. School.  Just after the resolution was passed the faculty received an email from the Provost Ralph Hexter that was very strongly saying he supported academic freedom on campus.

So that is where we stand now.  I am very pleased with the Provost’s statement.  At the same time I am still dismayed at the reported behavior of the Medical School administration.  And I think this issue needs to still get some air until there are repercussions for the Medical School actions …

Here are some related links and updates that I collected as the story has unfolded.



UPDATE: Some links of relevance

UPDATE 2: Some new links (6/8)

  • UC removes “In the media” page which linked to the Inside Higher Ed. story.
  • UC Davis Academic Senate passes three resolutions in relation to this case.  See here for full text.

UPDATE 7: 6/14

UPDATE 7: 6/15

UPDATE 8: 6/20

UPDATE 9: 6/25

UPDATE 10: 1/12/13

Well – finally some news.  Not sure what I think about it but at least something is moving forward.  A report was issued yesterday from a panel investigating this case.  
I have received a detailed email from Prof. Gregory Pasternack of UC Davis about the new “findings” from the report.  Pasternack was on the committee that issues the original report about this case.  He has this response to the new report:

1) Compared to the thorough 14-page analysis from the faculty investigation, the 2-page administrative review presents virtually no new information, contradicts the testimony of the Executive Associate Dean who said he was in fact responding to complaints against Dr. Wilkes, and completely ignores the totality of the threats all occurring peculiarly at the same time, creating a strong sense of retaliating when viewed as a whole. The faculty saw through thin excuses, while this review merely parrots and accepts them with no scrutiny or common sense. 

2) The administrative review claims a factual mistake in the timeline suggesting that the Executive Associate Dean wrote a key email before he was aware of Dr. Wilkes’ activities.  This is factually incorrect.  There is uncertainty about the timing of various emails (UC Davis does not keep historical emails, so a request for those went unfilled), but our report is very clear that Dr. Wilkes first raised his allegations to the Dean on September 16, 2010, well before the dates discussed by the administrative review.  Dr. Wilkes, other faculty, and the Dean were already well into the dispute when the Dean began retaliatory measures. Those measures continued over a period of time. The administrative review committee ignored this information. 

3) The administrative review appears to inappropriately downplay the seriousness of lawyers threatening faculty and fails to account for the fact that the lawyer was ordered by the administrators to send the threat to Dr. Wilkes.  Why are those administrators not held accountable for those orders?  According to the logic in the administrative review, if a person writes that they are not trying to interfere with a person’s academic freedom, then that grants free license to say and do anything, especially to violate faculty academic freedom. 

4) The fact that almost all administrative and legal personnel involved in the case have had adjustments to their University status since the Senate acted speaks louder than this poorly conducted and written review about what is going on. 

5) It is very disappointing that the administration will not apologize and move forward in a positive direction.

UPDATE 11:

UPDATE 12: 2/25/13

Just got this in email.  

Dear Academic Senate Members,
This message is being sent on behalf of Academic Senate Secretary, Abigail Thompson.  Please see the following link (http://academicsenate.ucdavis.edu/ra/RA-Meeting-Call-2013-02-28.pdf) to access the Representative Assembly Meeting Call forThursday’s (2-28-13) meeting.  You can also access RA information, meeting calls, and meeting summaries on the RA website (http://academicsenate.ucdavis.edu/repassembly.cfm).

On p9 of the document this is written:
Report to the Representative Assembly by CAFR – January 19, 2013
Last spring the Representative Assembly passed a series of resolutions related to academic freedom and the Provost sent a letter to the Senate in response. This report summarizes our analysis.

  1. In June 2012 the Representative Assembly unanimously condemned the use of letters from legal counsel to intimidate faculty: The provost has indicated that steps have been taken to prevent this, but stated that the actions of the administration cannot legally be described.
  2. In response to a thorough analysis by last year’s CAFR that found that the Medical School administration had impinged on the academic freedom of Michael Wilkes, the Representative Assembly unanimously requested in June 2012 that none of the actions threatened to punish Wilkes be carried out. To date, none of the actions have been carried out although none have been explicitly ruled out.
  3. In addition, the Representative Assembly unanimously passed a resolution calling for additional actions: an apology to Wilkes, training for medical school personnel on academic freedom and a report to the Representative Assembly with six months on the training program. The administration has elected not to do any of these things. The Provost has proposed a “town hall meeting” on academic freedom.
  4. The administration appointed a three person committee to examine the Wilkes case on their behalf. The committee’s report was provided with the letter from the Provost. There was only one new contention in the report; it called into question one piece of data in the CAFR report: the timing of one email threatening actions to be taken against Wilkes. Although put forward as a key issue, this is a secondary issue. Even assuming a revised timing of this email, the preponderance of evidence still supports the conclusions of the study conducted by CAFR last year and provided to the Representative Assembly, namely that the Medical School administration had impinged on the academic freedom of Michael Wilkes. 
——–
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.

——–

iEvoBio Last reminder: Deadline for iEvoBio Challenge Competitions is approaching

Via Hilmar Lapp

The deadline for submissions to the yearly iEvoBio Challenge is June 25, 2012, and is rapidly approaching! This is our last reminder. This year’s theme is "Synthesizing Phylogenies," and further information on criteria for challenge entries, how to submit them, and award amount can be found at http://ievobio.org/challenge.html.

Also, Biomatters Ltd is running the Geneious Challenge alongside iEvoBio’s competition. The goal of this challenge is to develop a new and exciting visualization or analysis plugin to Geneious Pro, using the public API. See http://ievobio.org/geneious_challenge.html for more information. The deadline for this competition is also June 25.

More details about the iEvoBio conference and program are available at http://ievobio.org. You can also find continuous updates on the conference’s Twitter feed at http://twitter.com/iEvoBio and Google+ page, or subscribe to the low-traffic iEvoBio announcements mailing list at http://groups.google.com/group/ievobio-announce.

iEvoBio 2012 is sponsored by the US National Evolutionary Synthesis Center (NESCent) and by Biomatters Ltd., in partnership with the Society for the Study of Evolution (SSE) and the Society of Systematic Biologists (SSB).

The iEvoBio 2012 Organizing Committee:
Hilmar Lapp, US National Evolutionary Synthesis Center (chair)
Robert Beiko, Dalhousie University
Nico Cellinese, University of Florida
Robert Guralnick, University of Colorado at Boulder
Rebecca Kao, Denver Botanic Gardens
Ellinor Michel, Natural History Museum, London
Nadia Talent, Royal Ontario Museum
Andrea Thomer, University of Illinois at Urbana-Champaign

Crowdsourcing help needed: how many microbes are brought into human GI tract via food? #microbiome

Quick but somewhat complex question here that came up at a recent meeting I went to – someone wanted to know:

How many microbes come into the human GI tract from outside sources (e.g., food)?

Other related questions:

  • How many cells /day?
  • How many are alive?
  • How many kinds come in?
  • How much flow through is there vs. digestion vs. colonization?

Note – I know there have been many studies of pathogens on food and how they get into the GI tract, but what about non pathogens?

Any references or #s would be very helpful.

Thanks

——–
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.

——–