Tag: Misc.

Winner of the "genome conference speakers should be male" award …

Presenters at the World Genome Data Analysis Summit.  Women highlighted in yellow.

  1. Richard LeDuc, Manager, National Center for Genome Analysis Support, Indiana University
  2. Gholson Lyon, Assistant Professor, Cold Spring Harbour Laboratory
  3. Christopher Mason, Assistant Professor, Cornell University
  4. Liz Worthey, Assistant Professor, Medical College of Wisconsin
  5. Garry Nolan, Professor of Genetics, Stanford University
  6. David Dooling, Assistant Director, Genome Institute, Washington University
  7. Peter Robinson, Senior Technical Marketing Manager, DataDirect Networks
  8. Thomas Keane, Senior Scientific Manager, Sequencing Informatics, Wellcome Trust Sanger Institute
  9. Eric Fauman, Associate Research Fellow, Pfizer
  10. Geetha Vasudevan, Assistant Director and Bioinformatics Scientist, Bristol-Myers Squibb
  11. Shanrong Zhao, Senior Scientist, Johnson & Johnson
  12. Bill Barnett, Director, National Center for Genome Analysis Support, Indiana University
  13. Zemin Zhang, Senior Scientist, Bioinformatics, Computational Biology, Genentech
  14. Christopher Mason, Assistant Professor, Cornell University
  15. James Cai, Head, Disease & Translational Informatics, Roche
  16. Eric Zheng, Fellow of Bioinformatics Science, Regeneron
  17. Monica Wang, Associate Director, Knowledge Engineering, Millennium
  18. Joachim Theilhaber, Lead Bioinformatics Research Investigator, Sanofi
  19. Francisco De La Vega, Visiting Scholar, Stanford University
  20. Don Jennings, Manager of Data Integration, Enterprise Information Management, Eli Lilly
  21. Deepak Rajpal, Senior Scientific Investigator, Computational Biology, GSK
  22. Mark Schreiber, Associate Director, Knowledge Engineering, Novartis

So that is a ratio of 19:3 for a whopping 13.6% women.  Please – I beg of you – if you are organizing a conference give some thought to the diversity of speakers.  In my experience the best conferences have always ended up being ones with highly diverse speakers.  These conferences were good probably because the organizers put a lot of thought into who to invite to speak, rather than just inviting either big names or people that one knew in some way.

UPDATE: It has been pointed out that I listed one person (Chris Mason) twice — so it is only an 18:3 ratio.  Phew.  Much better.

For other posts on this topic see

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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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Velasquez-Manoff opinion piece in the NY Times on autism, parasites & inflammation; nice ideas; not enough caveats

There is a very interesting “Opinion” piece in the New York Times today: Immune Disorders and Autism – NYTimes.com.  By Moises Velasquez-Manoff is details some recent work that the author believes relates to autism and a variety of other human ailments with an autoimmune connection.

The general logic/key points seem to be as follows:

  • Some autism cases look like a form of inflammatory diseases with the immune system overactive (inflammation on high, anti-inflammation on low, or some combination thereof)
  • Infection of a mother during pregnancy increases the risk of having a child with autism.
  • In animal models, inducing inflammation in the mother (even without an infection) leads to an increased risk of behavioral “problems” in her offspring
  • Inflammatory and/or autoimmune diseases (e.g., asthma) have increased in incidence along with autism.
  • If a mother has automimmune or inflammatory diseases such as rheumatoid arthritis celiac disease she has a higher risk of having a child with autism.  Similarly if a mother has allergies or asthma during the second trimester, there is a higher risk of having children with autism.  
  • Many automimmune and inflammatory disorders and autism are all more prevalent is the developed world.
  • The developed world is generally cleaner that the developing world.  
  • There are many fewer parasites in people in the developed world.
  • Parasites are known to suppress inflammation.
  • Therefore, we may be able to stop/limit autism, asthma, and other inflammatory diseases by purposefully infecting people with parasites from our evolutionary past. 

Now, personally, I like the general hypothesis here.  It makes complete sense.  But alas, it is suffers from this issue that is spreading almost as fast as these diseases – a lack of a discussion of the distinction between correlation and causation.  I have been obsessing about this a bit recently with studies of the microbiome.   Overall, I do like this current article.  It mixes human epidemiological studies with controlled animal studies with discussion of conceptual models.  But alas there is really no discussion of the challenges if disentangling correlations vs. causation. And I think it is a bit dangerous in the latter parts with the jump to potentially curing these various ailments by purposeful infection with parasites.  Again, I like the idea.  But a few caveats would have been nice.  I am glad it was marked as an opinion piece but even when one states an opinion about a medical issue, one can still say “there are reasons why this might not be true .. such as …”.  Too bad that wasn’t done here.

UPDATE – Emily Willingham has written a VERY detailed critique of the article that I think everyone interested in anything related to this topic should read: Emily Willingham: Autism, immunity, inflammation, and the New York Timeswww.emilywillinghamphd.com.

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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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Notes from some recent meetings about microbiology of the built environment

Quick post here.  At the microBEnet site that I run we have posted some notes, slides, videos and other information from a few recent meetings on the topic of “microbiology of the built environment” that may be of interest so I am posting links here

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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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"Genomics: the Power and the Promise" meeting – could be called "Men Studying Genomics" instead

Just got another email advertising this meeting: Genomics: the Power and the Promise.  Organized by Genome Canada and the Gairdner Foundation.  And, well, though I love some of the things Genome Canada has done, this conference really stick in my craw in the wrong way. Why?  It has a serious male speaker overabundance.  Here is the list of speakers:

Day 1 

  1. Pierre Muelien
  2. John Dirks
  3. Gary Goodyear
  4. Eric Lander
  5. Craig Venter
  6. Philip Sharp
  7. Svante Paabo
  8. Tom Hudson
  9. Peter Jones
  10. Stephen Scherer
  11. Michael Hayden
  12. Bertha Maria Knoppers

Day 2

  1. Stephen Mayfield
  2. Elizabeth Edwards
  3. Curtis Suttle
  4. Peter Langridge
  5. Michel Georges
  6. William Davidson
  7. Klaus Ammann

That is 17:2 male: female ratio. That is one female speaker per day.  Not impressive.

On Day 2 there are two panels (which generally I do not count as “speakers” but at least there are a few more women on these):

  • Panel 1: Sally Aitken, Vincent Martin, Elizabeth Edwards, Curtis Suttle, Gerrit Voordouw, Steve Yearley
  • Panel 2: William Davidson, Martine Dubuc, Isobel Parkin, Graham Plastow, Curtis Pozniak, Peter Phillips 

So if you count these that then comes to a ratio of presenters of 25: 6.  Do I want quotes for meetings?  No, but given that the ratio of men: women in biology is close to 1:1 this suggests to me some sort of bias.  Where does this bias come from?  I don’t know.  Could be at the level of who gets invited.  Could be at the level of who accepts.  Could be some non obvious criterion for selecting speakers that leads to a bias towards men.  I don’t know.  But I personally think they could do better.  And I note – they could probably do better in terms of other aspects of diversity of speakers, but I am focusing here just on the male vs. female ratio.  Again, I am not suggesting one should have quotas for all meetings but at the same time, a 17:2 male to female speaker ratio suggests something could use some working on.

As a side story I decided to look at some past conferences sponsored by Genome Canada.  I worked my way down the list … see below:

  • 2008 Joint IUFRO-CTIA International conference. Speakers: 8:2 male: female
  • 6th Canadian Plant Genomics Workshop Plenary Speakers 8:2
  • 8th Annual International Conference of the Canadian Proteomics Initiative.  See below.  32:2 male to female.  I have no idea what the ratio is in the field of proteomics but this is a very big skew in the ratio.  94% male.  
    1. Leigh Anderson (Plasma Proteome Institute)
    2. Ron Beavis (UBC)
    3. John Bergeron (McGill)
    4. Christoph Borchers (UVic)
    5. Jens Coorssen (U Calgary)
    6. Al Edwards (U Toronto)
    7. Andrew Emili (U Toronto)
    8. Leonard Foster (UBC)
    9. Jack Greenblatt (U Toronto)
    10. Juergen Kast (UBC)
    11. Gilles Lajoie (U Western Ontario)
    12. Liang Li (U Alberta)
    13. John Marshall (Ryerson)
    14. Susan Murch (UBC Okanagan)
    15. Richard Oleschuk (Queens)
    16. Dev Pinto (NRC)
    17. Guy Poirier (Laval)
    18. Don Riddle (UBC)
    19. David Schreimer (University of Calgary)
    20. Christoph Sensen (University of Calgary)
    21. Michael Siu (York)
    22. John Wilkins (University of Manitoba)
    23. David Wishart (University of Alberta)
    24. Rober McMaster (Universiyt of British Columbia)
    25. Peter Liu (University of Toronto)
    26. Christopher Overall (Universiyt of British Columbia)
    27. John Kelly (NRC, Ottawa)
    28. Joshua N. Adkins (Pacific Northwest National Laboratory, USA)
    29. Dustin N.D. Lippert (University of British Columbia)
    30. David Juncker (McGill University)
    31. Jenya Petrotchenko (University of Victoria)
    32. Detlev Suckau (Bruker Daltonik GmbH)
    33. Peipei Ping (University of California)
    34. Robert McMaster (University of British Columbia)
I couldn’t bear to go on any further.
Now – note – I am not accusing anyone of bias here.  But I do think it might be a good idea for Genome Canada to put some more effort into figuring out why the conferences they sponsor have such skewed ratios.  And perhaps they can try to do something about this.  For more on this issue from my blog see
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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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Referring to 16S surveys as "metagenomics" is misleading and annoying #badomics #OmicMimicry

Aargh.  I am a big fan if of ribosomal RNA based surveys of microbial diversity.  Been doing them for 20+ years and still continue to – even though I have moved on to more genomic/metagenomic based studies.  But it drives me crazy to see rRNA surveys now being called “metagenomics”.

Here are some examples of cases where rRNA surveys are referred to as metagenomics:

I found these examples in about five minutes of googling.  I am sure there are many many more.  
Why does this drive me crazy?  Because rRNA surveys focus on a single gene.  They are not gnomicy in any way.  Thus it is misleading to refer to rRNA surveys as “metagenomics”.  Why do people do this?  I think it is pretty simple.  Genomics and metagenomics are “hot” topics.  To call what one is doing “metagenomics” makes it sound special.  Well, just like adding an “omic” suffix does not make ones work genomics – falsely labeling work as some kind of “omics” also does not make it genomics.
Enough of this.  If you are doing rRNA surveys of microbial communities – great – I love them.  But do not refer to this work as metagenomics.  If you do, you are being misleading, either accidentally or on purpose.    So I think I need a new category of #badomics – “Omic Mimicry” or something like that …
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Note – this post was spurred on by a Twitter conversation – which is captured below (note – I am certain I have complained about this before but cannot find a record of it …)

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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.

——–

How to find an Open Access journal for submitting your paper(s) #Jane #DOAJ

Got asked a question on Twitter that seems worthwhile to post here

Basically what I was suggesting was two possible steps. The first is to search the Database of Open Access Journals which is a great place to browse to see what the possibilities are. Another great resource/tool is JANE – the Journal/Author Name Estimator. I love Jane and use it all the time (if interested also see the paper on Jane here). The default screen for Jane looks like this:

And you can certainly use the default options. Just type in some keywords, or copy and paste a document or abstract of a paper and select “Find Journals” and voila you get some suggested journals which match your text. So for example if I paste in “evolution genomes novelty phylogeny microbes” and search for journals I get some useful suggested journal matches

And you can also select the “show articles” option which will, well, show you some of the article matches
Also you can even export the citations, which is a nice option for adding references to various collections you might have or for looking later.
You can also look for authors or articles that match your text/keywords instead of journals.  The “find authors” option is great for searching for possible reviewers if you are handling the review of a paper (or a grant). 
But my favorite part of Jane is what you can do with the “Show extra options” option. This is the menu you get
This allows one search for kinds of articles as well as for kinds of access.  For example, if I select “only journals with immediate access” I get a list of places I would submit papers
I am sure there are other resources out there but I particularly like these two … Any other suggestions from the world out there?
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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.

——–

Wow – who would have thought? Microbes are central to election in Wyoming

Fascinating story from a microbiology point of view: Republican candidates disagree on water rights in Yellowstone.  Seems that one of the three main candidates in this Republican primary election is focusing partly on microbes.  Here are some microbial quotes from the story:

“Jennings fervently believes that the microbes found in Yellowstone National Park’s boiling waters should be working for Wyoming, generating royalties to help fund state programs. The notion has received criticism from Anderson and Radosevich.”

“Radosevich simply refuted the notion that the state should seek monetary gain from Yellowstone microbes in the first place” 

“Jennings maintains that Wyoming is sitting on an “enormous bank of microbes” that have yet to be discovered. “

See more on this issue:

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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.

——–

The Ballad of #UCDavis from Aaron Heuckroth

The Ballad of UC Davis from the brilliant and talented Aaron Heuckroth.


Hat tip to the Davis Patch.

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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.

——–

Some articles on the uses and misuses of the "impact factor"

Collecting some articles and blog posts on impact factor uses and misuses.  Inspired by this blog post: Sick of Impact Factors | Reciprocal Space

  • Created a Mendeley Group on this topic

http://www.mendeley.com/groups/2486431/impact-factor/widget/29/10/

——–
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.

——–

MMMMM: Microbes, Metagenomics, Minnesota, Mississippi, & Morrison

A really cool project is discussed in an issue of the University of Minnesota News: Microbes in the Mississippi : UMNews : University of Minnesota.  I found out about it through an automated web search I have running in the background via Google.  The news story discusses a project in which scientists from U. Minnesota are sampling the microbes in the Mississippi River using metagenomics.  Their data is (apparently) deposited into the IMG database and shared with the world (though I note – no link is provided).  This is exactly the kind of new project that cheap sequencing enables …  I hope to see many many more like this …

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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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