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

Good morning to my Twitter SPAM followers – is Twitter even trying to stop this?

Here are some of my SPAM followers from this morning … again … all pointing to blog.livedoor.jp addresses.  Twitter still does not seem willing or able to do anything about this.  Annoying.

I and others have written about this extensively and still no response or action from Twitter.
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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.

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MoreCite Feed from my Google Citations Page

Just got an email from someone at MoreCite.com describing a simple widget they have made to display information from one’s Google Citation page. So I took the bait .. and two minutes later I have a feed: http://morecite.com/js/morecite.min.js This is not an endorsement of MoreCite.Com. I know very little of what they are about. But I like the little widget …

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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.

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For those interested … storification of twitter discussion criticizing NY Times article on Venter cell model

Storification is here and below.
http://storify.com/phylogenomics/critiques-of-ny-times-story-on-venter-cell-model.js[<a href=”http://storify.com/phylogenomics/critiques-of-ny-times-story-on-venter-cell-model” target=”_blank”>View the story “Critiques of NY Times story on Venter Cell Model” on Storify</a>]

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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.

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#UCDavis neurosurgeons conducted experimental surgery w/o IRB approval

Not really sure what to say about this other than that this story should be read by many/all who are interested in medical research and/or UC Davis: 2 UC Davis neurosurgeons accused of experimental surgery are banned from human research – Investigations – The Sacramento Bee.

UPDATE 7/23.  Added a summary: Two UC Davis neurosurgeons were treating terminally ill brain cancer patients with an unapproved, experimental treatment that is referred to as “Probiotic Intracranial Therapy for Malignant Glioma”.  The treatment involved purposefully infecting patients brains with a bacterium Enterobacter aerogenes apparently because of prior anecdotes and case reports that suggested that patients with these brain cancers who also had brain infections might live longer than those with the cancer but without the infection.  According to the article, there was an investigation at UC Davis into the practices of the surgeons.  It was determined by UC Davis that they did not have IRB approval to carry out the treatments and that there were some other issues with the practice going on.  At the conclusion of the investigation UC Davis wrote a letter to the FDA detailing the case and has banned the two neurosurgeons from performing medical research on humans.  Read the article for much more detail and see the link below.

Many interconnected issues in here involving IRB approval, human experimental treatments and informed consent, UC Davis, and even “probiotics”.  Still taking it all in …  Uggh …

Other stories posted in the SacBee at the same time:

See also

UPDATE 7/22/12. Some tidbits to consider
  • The doctors used the bacterium Enterobacter aerogenes for the treatment.  It wear obtained from ATCC and grown by a graduate student at UC Davis.
  • The use of the bacterium for human treatments violated the ATCC MTA.
  • It is unclear from the details here why this bacterial strain/species was selected.  But I assume it is related to the referenced Neurosurgery article (see more below).
  • The hypothesis that purposefully causing an infection may help glioblastoma patients seems to come from the observation that patients with glioblastoma w/ postoperative infections have better survival than those who do not get infections.  This could be due to many many factors jumping to purposefully causing infections with E. aerogenes seems a big big jump.
  • It would be nice to know more about the statement “Early this year, as required by University policy Drs. Muizelaar and Schrot submitted a Record of ~Invention for the bacterial intervention to UCD’s technology transfer office.” in the letter from UCD to the FDA.  Was this just a formality or were the surgeons looking to patent/protect the bacterial treatment method?
  • The Neurosurgery article discussing infection and glioblastoma may be “Long-term Remission of Malignant Brain Tumors after Intracranial Infection: A Report of Four Cases” Neurosurgery: March 1999 – Volume 44 – Issue 3 – pp 636-642.  This reported that some of the patients with infections that seemed to have a longer survival with glioblastoma were infected with E. aerogenes.
    • “In three of the cases described above, Enterobacter aerogenes was recovered from microbial cultures. Whether the presence of Enterobacter aerogenes was coincidental or whether this organism plays an important role in tumor defense is not known and cannot be proven from the cases reported. “
  • See also
UPDATE 2
UPDATE 3 – some papers on bacterial infections and glioblastoma and other cancers
UPDATE 4: Some other news stories (not sure how many are independent)
UPDATE 5: 7/23 12:33 AM
  • Biocrime or a Passion to Save a Life?.  This pointed me to the article below:
  • A key article of interest: Post-operative infection may influence survival in patients with glioblastoma: simply a myth?: Glioblastoma, infection and survival from 2011. The article casts some doubt on the basis for the treatment used here
    • Citation: De Bonis P, M D AA, M D GL, de Waure C, Mangiola A, Pettorini BL, Pompucci A, Balducci M, Fiorentino A, Lauriola L, Anile C, Maira G. 2011. Post-operative infection may influence survival in patients with glioblastoma: simply a myth?: Glioblastoma, infection and survival. Neurosurgery. 2011 Oct;69(4):864-8; discussion 868-9.
    • “One of the myths that continues to be perpetrated in neurosurgery relates to the observation that a postoperative infection may actually confer a survival advantage in patients with malignant glial tumors”
    • The take-home message of this study, which can be applied to any aspect of neurosurgery, is to do everything possible to prevent a postoperative wound or cavity infection. The association between infection and prolonged survival is not definitive; we acknowledge the considerable difficulties in undertaking this type of study in a retrospective manner in view of the numerous clinical variables. A prospective randomized study on this subject is clearly not possible. Nevertheless, we believe the results of this study are important and can be used as a stimulus for further multicentric studies (to increase the number of patients) or for experimental studies using genetically modified bacteria for the treatment of GBM.
  • Also see The survival impact of postoperative infection in patients with glioblastoma multiform from 2009.
    • “In this single-center study, postoperative infection did not confer any survival advantage in patients with glioblastoma multiforme”. 
    • Available free online here. 
    • “This study did not show a causal relationship between postoperative infection and prolonged survival in patients with GBM. Although targeted immunotherapy may provide antitumoral effects, simple infection does not appear to do so. Modern aseptic and antiseptic surgical techniques continue to be integral to the care of patients with gliomas.“
  • Also see  Cancer J. 2012 Jan-Feb;18(1):59-68. Immunotherapy for the treatment of glioblastoma. Thomas AA, Ernstoff MS, Fadul CE. (though I cannot seem to be able to get a copy ..)

    UPDATE 6: 7/23 10 AM – some info. on UC Davis IRB, Med School, etc

      UPDATE 6: 7/23 3: 45 PM Some news stories/blog posts
      UPDATE 7: 7/24 Some news stories/blog posts
      UPDATE 8: Some more stories
      UPDATE 9: SacBee Editorial calling for Muizelear to step down as Chair
      • The Sac Bee has an editorial today calling for the doctor involved in this issue to step down as chair of the Neurosurgery department.  Some quotes below
      • “Experimentation on terminal patients requires a specific set of protections for good reason. People who are, quite literally, on death’s doorstep are extremely vulnerable, and therefore not always able to give informed consent.“
      • “University officials conceded that “systemic issues” within the medical center may have contributed to errors made and that “additional measures designed to avoid future confusion” have been put in place.”
      • “Curiously, even after it was imposed last fall, the university named Muizelaar to fill its new Julian R. Youmans endowed chair in neurological surgery. The donor specified, university officials explained, that the chair be filled with the head of the department, a fact that begs the question: Why is Muizelaar still chairman of the department?”
      UPDATE 9: some new stories
      UPDATE 10: Nature News Story
      UPDATE 11: Muizelaar steps down as chair of department, at least temporarily
      • UC Davis neurosurgeon department chair steps down pending …
        • “One advocate for ethical human subjects research questioned the university’s decision to keep the matter in-house instead of seeking outside review. “The time is long gone for another internal investigation,” said Elizabeth Woeckner, founder and director of Citizens for Responsible Care and Research, or CIRCARE. The nonprofit group works to improve protections for human subjects in research. Woeckner called the doctors’ work on the patients – intentionally infecting them with bacteria restricted to use in lab rats only – as “the worst thing I’ve seen in my 12 years with CIRCARE.””
      UPDATE 12 – September 7, 2012 – some new news stories on Federal investigations
      UPDATE 13: December 11, 2012 – Federal investigation at UC Davis, Resignation of UC Davis Dean of Medicine, more
      UPDATE 14: December 13, 2012 
      UPDATE 15: December 21, 2012
      UPDATE 16: August 15, 2015
      Well, many things have happened since 2012 – here are some stories to look at
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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.

      ——–

      "Life on Man" – amazing book on human associated microbes

      Just got this book by Theodor Rosebury in the mail: The Tree of Life Store – Life on Man.

      I ordered it a few days ago after someone named Richard Montgomery posted a comment about it in relation to my “Human microbiome” talk that is posted at TED.

      Just starting the book but it is awesome so far.  Definitely worth trying to get a copy.  Though it is out of print, I found many copies online … //ws-na.amazon-adsystem.com/widgets/q?ServiceVersion=20070822&OneJS=1&Operation=GetAdHtml&MarketPlace=US&source=ac&ref=tf_til&ad_type=product_link&tracking_id=thtrofli-20&marketplace=amazon&region=US&placement=0670427934&asins=0670427934&linkId=UY6Y5ADMTK4HG6FI&show_border=true&link_opens_in_new_window=true

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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.

      ——–

      Field / Lab Technician Needed for Studies of eelgrass genetic diversity

      Field / Lab Technician Needed for Studies of eelgrass genetic diversity

      We are searching for a technician to join an interdisciplinary project on effects of genetic diversity on eelgrass ecosystem functioning at the UC Davis Bodega Marine Lab. The position will assist PIs and a graduate student with measuring nutrient uptake, assessing interclonal competition, and other biochemical measurements in the lab and help plant and maintain various experiments in outdoor tanks and in the field. Early morning and late night work will be needed periodically to accommodate field and lab schedules. General experience with field and laboratory ecological research required. Must also have good work ethic, organizational skills, general computer skills (excel, word), and an interest in ecology or marine biology. Experience / skill in any of the following specific areas is desirable (though not absolutely required): nutrient analysis (nitrate, ammonium), basic mechanical skills (e.g., pumps, simple plumbing), scientific diving, marine ecology, analytical instruments (autoanalyzer, elemental analyzer).

      Position will be located at the Bodega Marine Lab in Bodega Bay, CA in the labs of Jay Stachowicz and Susan Williams. Questions about the position should be directed to Jessica Abbott at jmabbott. For information about the marine lab see: http://www.bml.ucdavis.edu. For information about research in the Stachowicz and Williams lab see their websites: http://www.eve.ucdavis.edu/stachowicz/ and http://bml.ucdavis.edu/research/faculty/susan-williams/. The full time position is available starting in August 2012 and for up to 2 years. Salary approximately $34,000 per year and includes health benefits.

      To apply, send the following material to Jessica Abbott at jmabbott:
      (1) Cover letter that outlines interests, previous research experience, any relevant skills, career goals, and earliest possible start date; (2) Unofficial copy of college transcript or list or relevant coursework with grades earned; (3) Resume or curriculum vitae and (4) the names, email address and phone number of 2 references. Applications must be received by August 5 to receive full consideration, but the position will remain open until filled.

      Twitter seems to have lost complete control of some spam

      Aaarrrrggg … this is driving me crazy.  For over a month now I have been seeing 10-20-30 or more new followers a day on Twitter that are some sort of SPAM.

      For example, a few minutes ago I looked at my most recent followers:

      And when I look at them in more detail I see many of them are simply posting links to some SPAMMY sites at the domain “blog.livedoor.jp”.  For example

      and

      and many many many many more.  They are all like this with links to some spammy site at blog.livedoor.jp.  It is so easy to identify these … but it is a pain.  Why can’t Twitter get a handle on this?   I mark them as SPAM – day after day after day.  And more come. Uggh.

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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.

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      Exit seminar for Jenna Morgan Lang in my lab: 7/20 10 am

      PhD Exit Seminar Announcement

      Jenna Morgan Lang
      (Microbiology Graduate Group)

      Friday, July 20, 2012
      10:00 a.m.

      Room 4202, GBSF

      “Exploring Microbial Community Composition and Genome Evolution Using Environmental and Comparative Genomics”

      My "human associated microbes" talk now available on TED site (w/ transcripts too).

      My TedMed talk is now on Ted.Com. See below. Some interesting comments too – have been trying to respond to most — even the unusual ones.

      http://video.ted.com/assets/player/swf/EmbedPlayer.swf

      Plus there is now a transcript available in English and German. And the transcripts are hot linked to the portions of the video …

      Thanks to Tedmed for allowing this and to TED to posting the talk.  Plus the folks at TED re-edited the talk and added some more camera angles for the part where I tossed giant stuffed microbes into the crowd …

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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.

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