Tag: Misc.

#UCDavis Prof. Dawn Sumner video interview on being involved in Mars Curiosity Rover landing

I am getting really excited about the upcoming Curiosity landing on Mars. So cool that Dawn Sumner – Geology Prof. from UC Davis is going to be involved …
 

Also check out:

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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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Nice new memory efficient metagenome assembly method from C. Titus Brown –

Interesting new #OpenAccess PNAS paper from C. Titus Brown: Scaling metagenome sequence assembly with probabilistic de Bruijn graphs.  Of course, if you follow Titus on Twitter or his blog you would know about this already because not only has he posted about it but he posted a preprint of the paper on arXiv in December.

Check out the press release from Michigan State.  Some good lines there like “Analyzing DNA data using traditional computing methods is like trying to eat a large pizza in a single bite.”

A key point in the paper: “The graph representation is based on a probabilistic data structure, a Bloom filter, that allows us to efficiently store assembly graphs in as little as 4 bits per k-mer, albeit inexactly. We show that this data structure accurately represents DNA assembly graphs in low memory.” This is important because right now most assemblers for genome data use a ton of memory.

Anyway the software behind the paper is available on GitHub here.  Assemble away.

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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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William Shatner, Mars, Curiosity, Rover … fun fun fun

William Shatner narrates video detailing how Curiosity will land on Mars next week http://cdn-akm.vmixcore.com/vmixcore/js?auto_play=0&cc_default_off=1&player_name=uvp&width=512&height=332&player_id=1aa0b90d7d31305a75d7fa03bc403f5a&t=V0xL7FpdMBTgI9wbokivyCDQbYr3dNMyMc Hat tip to Dawn Sumner, UC Davis Geology professor working on Curiosity mission, for pointing me to this. Don’t like that? Well, here is a narration by Wil Wheaton http://cdn-akm.vmixcore.com/vmixcore/js?auto_play=0&cc_default_off=1&player_name=uvp&width=512&height=332&player_id=1aa0b90d7d31305a75d7fa03bc403f5a&t=V0J_fCVbhIlC6m5frWM2NxUQEaE4C8GCK_

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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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Posts from #microBEnet that may be of interest

Quick post here – posting links to recent blog posts on the microBEnet blog that may be of interest here.  The microBEnet blog is part of the microBEnet project that I run on microbiology of the built environment.

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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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Not a #badomics word but – "Evolutionary Systems Biology" is – well – pretty complex

Just saw the title of this article Evolutionary Systems Biology: Historical and Philosophical Perspectives on an Emerging Synthesis by Maureen A. O’Malley in Advances in Experimental Medicine and Biology, 2012, Volume 751, 1-28, DOI: 10.1007/978-1-4614-3567-9_1.  And my first thought was “Hmmm – WTF is Evolutionary Systems Biology“.  Given that I am still unsure what Systems Biology is exactly I figured – this could be a doozy.  Thus I perused the abstract:

According to the abstract

Systems biology (SB) is at least a decade old now and maturing rapidly. A more recent field, evolutionary systems biology (ESB), is in the process of further developing system-level approaches through the expansion of their explanatory and potentially predictive scope. This chapter will outline the varieties of ESB existing today by tracing the diverse roots and fusions that make up this integrative project. My approach is philosophical and historical. As well as examining the recent origins of ESB, I will reflect on its central features and the different clusters of research it comprises. In its broadest interpretation, ESB consists of five overlapping approaches: comparative and correlational ESB; network architecture ESB; network property ESB; population genetics ESB; and finally, standard evolutionary questions answered with SB methods. After outlining each approach with examples, I will examine some strong general claims about ESB, particularly that it can be viewed as the next step toward a fuller modern synthesis of evolutionary biology (EB), and that it is also the way forward for evolutionary and systems medicine. I will conclude with a discussion of whether the emerging field of ESB has the capacity to combine an even broader scope of research aims and efforts than it presently does.

I am not sure what to say here.  The author has published some interesting work previously on philosophical issues in biology.   But from the abstract – well – I am pretty lost.  It seems that ESB covers a lot of ground.  First – systems biology – whatever it means –  itself is pretty broad.  And then on top of that, ESB apparently covers even more than SB.  Still not sure what ESB is — I am torn about whether it could be interesting or completely flaky.  I am (as many know) a big fan of adding evolutionary approaches to just about any area of biology.  So that alone makes me think about reading the paper to see whether there is any there there.  But alas, I do not have access, so I am going to have to move on to something else.

Some comments from the web on this paper

https://twitter.com/caseybergman/status/229477100069978112

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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
  • 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 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 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 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.

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      "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.

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      Three talks, 1.5 days at #ISMB … phylogeny, phylogenomics, open science and more

      Gave three talks in 1.5 days here in Long Beach as part of the satellite meetings associated with the “Intelligent Systems for Molecular Biology” (ISMB) 2012 Conference. I will write more about the meeting and the craziness of giving three very different talks in 1.5 days. But for now I wanted to at least get my talks posted here since I posted the slides to slideshare and recorded the audio in synch with the slides and posted these “slideshows” to YouTube. Here are the talks below:

      Talk 1 for the “Bioinformatics Open Source Conference” BOSC2012.  Was asked to talk about Open Science … so … I did …

      Slides: Jonathan Eisen talk on “Open Science” at #BOSC2012 #ISMB

      View more presentations from Jonathan Eisen

      Slideshow with audio:
       

      Talk 2 for the Student Council Symposium SCS2012. Sort of supposed to be a career guidance discussion so I geared my talk on the lines of “lessons learned” …


      Slides:Jonathan Eisen talk for #SCS2012 at #ISMB “Networks in genomics and bioinformatics: from phylogeny to Twitter”

      View more presentations from Jonathan Eisen

      Slideshow with audio:

      Talk 3 for the “Automated function prediction” AFP2012 satellite meeting.  I decided to talk about phylogenetic and phylogenomics approaches to functional prediction …

      Slides:Jonathan Eisen talk “Phylogneomic approaches to functional prediction”a #AFP2012 #ISMB

      View more presentations from Jonathan Eisen

      Slideshow with audio:

      http://storify.com/phylogenomics/jonathan-eisen-talks-at-ismb-satellite-meetings.js[<a href=”http://storify.com/phylogenomics/jonathan-eisen-talks-at-ismb-satellite-meetings” target=”_blank”>View the story “Jonathan Eisen @phylogenomics talks at #ISMB Satellite Meetings” 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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      My new paper in #Gigascience: #Badomics words and the power and peril of the ome-meme

      I have a new paper in the new Open Access journal Gigascience:  GigaScience | Full text | Badomics words and the power and peril of the ome-meme.  It is basically a text version of my obsession with #badomics words.

      It was inspired by a paper also in this first issue of Gigascience The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome by Daniel McDonald, Jose C Clemente, Justin Kuczynski, Jai Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, and J Caporaso.

      For more on my obsession with badomics words see some of these earlier posts:

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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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      Posted to Twitter, FB, etc but had to post to blog too: best genomics Venn Diagram ever

      Words do not do this justice.  This is just stunning.
      From here.
      Ref: “The banana (Musa acuminata) genome and the evolution of monocotyledonous plants” Nature 2012 doi:10.1038/nature11241
      Also see this Storify.
      ——–
      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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