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

Fecal transplants in the news

CNN has a story on a fecal transplant case: Little-known fecal transplant cures woman’s bacterial infection – CNN.com.  It is worth a look and if you want to laugh (sometimes in pain, sometimes for jokes) read the comments. Some other recent stories on this topic include

And the CNN story got picked up by Reddit
As many know – I have been talking / writing about such treatments a bit recently.  I discussed it in my Tedmed talk (which is now on Ted).

http://video.ted.com/assets/player/swf/EmbedPlayer.swf And I have a blog post with background and links on the topic.

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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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The biggest academic scam ever (caution – attempt at humor 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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Eisen Lab Paper.Li Magazine

Playing around with Paper.Li. Took feeds from the blogs and Twitter profiles of people in my lab. Seems to come out OK … http://widgets.paper.li/javascripts/sr.embeddable.js Paperli.PaperFrame.Show({ id: ‘6f0c6ad8-8b14-41e0-b46a-1a7592d3eadb’, width: 390, height: 480, background: ‘#ECECEC’, borderColor: ‘#DDDDDD’ })

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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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Fall 2012 C-DEBI Call for Proposals Deadline MONDAY 10/1/12

Forwarding this email to this blog:

Don’t forget! C-DEBI is interested in funding your research and education and outreach – with entrainment of new researchers not previously funded by C-DEBI as a major consideration! Proposals are due Monday 10/1/12.

Fall 2012 Calls For Our Research, Education and Outreach Grants are Now Posted! Apply now for C-DEBI funds in support of deep biosphere research, education and outreach. C-DEBI supports Small Research Grants and Small Education and Outreach Grants up to $50,000. C-DEBI also supports Fellowships for Graduate Students and Postdoctorals! Proposals are due October 1, 2012. See each opportunity for specific deadlines.

Lake Arrowhead Microbial Genomes Meeting 2012 Speaker Gender Ratio #LAMG12

Got some questions about the Lake Arrowhead Microbial Genomes 2012 Meeting in regard to gender ratio of speakers and organizers, after I have been complaining about ratio at other meetings.  Here is the full list of speakers and organizers for this meeting.  Women in bold.
Organizers:
  1. Jeffrey H. Miller
  2. Jonathan Eisen
  3. Ashlee Earl
  4. Lisa Raleigh
So the organizers are a 50-50 split.
Speakers (in order)
  1. Jonathan Eisen
  2. Nina R. Salama
  3. Frederic Bushman
  4. Kristine Wylie
  5. Janet K. Jansson
  6. Forrest Rohwer
  7. Curtis Huttenhower
  8. Tanja Woyke
  9. Maomeng Tong
  10. Jeffrey Cox
  11. Susannah Tringe
  12. Julian Parkhill
  13. Rustem F. Ismagilov
  14. Gautam Dantas
  15. Pamela Yeh
  16. Mike Gilmore
  17. Lance B. Price
  18. James Meadow
  19. Jason E. Stajich
  20. Laura Sauder
  21. Tara Schwartz
  22. Susanna Remold
  23. Bernhard Palsson
  24. Anca Segall
  25. Trent Northern
  26. Rick Morgan
  27. Beth Shank
  28. Morgan Langille (added)
  29. Anthony Fodor (added)
  30. Peter Karp
  31. Tatiana Tatusova
  32. Timothy Harkins
  33. Katrine Whiteson
  34. Mallory Embree
  35. Varum Mazumdar
  36. Abigail McGuire
  37. Ee-Been Goh
  38. Shota Atsumi
  39. Howard Xu

So 37 39 speakers, 16 of which are women.  So that comes to 43.2 41%.

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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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Storify for Lake Arrowhead Microbial Genomes #LAMG12 Meeting

Meeting went well.  Here is a storification of it:

http://storify.com/phylogenomics/lake-arrowhead-microbial-genomes-2012-lamg12.js?template=slideshow[View the story “Lake Arrowhead Microbial Genomes 2012 #LAMG12” on Storify]

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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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Google Scholar has search by date option – a good thing

Woohoo.  Just discovered a cool (I think new) thing.  Was looking for a link to a new publication of mine.  And I searched Google Scholar

That gets my publications but they are sorted by citation number which alas does not pull up new publications.  So I went to click on the “Since 2012” button I usually click on

And I noticed something I have not noticed before (and that I think must be pretty new):

Woohoo – a full sort by date option.  And so I clicked it and indeed it did work.

This will make Google Scholar much more useful for certain purposes.  This – along with other new features such as the Google Scholar “Updates” system is giving me hope that Google will continue to expand the tools/features of Google Scholar.

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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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Fun science art example: Jennifer Welsh on Zachary Copfer glowing microbe drawings

Microbiology art pops up again.  This time in this story from Jennifer Welsh: Galaxies And Faces Drawn With Glowing Bacteria – Business Insider .  For more see the artist Zachary Copfer’s website here: http://sciencetothepowerofart.com.  Other stories about Copfer are popping up too – not sure if their is some publicity blitz going on or not but see below for examples:

ut whatever is going on the art is worth checking 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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Upcoming on phyloseminar "Inferring macroevolutionary processes based on phylogenetic trees"

See phyloseminar.org home for more detail.
Next talk
Inferring macroevolutionary processes based on phylogenetic trees”
Tanja Gernhard Stadler (ETH Zurich)

Phylogenetic trees of present-day species allow inference of the rate of speciation and extinction which led to the present-day diversity. Classically, inference methods assume a constant rate of diversification, or neglect extinction. I will discuss major limitations of this null model and will present a new framework which allows speciation and extinction rates to change through time (environmental-dependent diversification), with the number of species (density-dependent diversification), and with a trait of a species (trait-dependent diversification). For the latter model, particular focus is given to the trait being the age of a species. Issues arising in empirical data analysis, such as incomplete taxon sampling, model selection, and confidence interval estimation, will be discussed. The methods reveal interesting macroevolutionary dynamics for mammals, birds and ants, and can easily be applied to other datasets using the R packages TreePar and TreeSim available on CRAN.

West Coast USA: 10:00 (10:00 AM) on Wednesday, September 19
East Coast USA: 13:00 (01:00 PM) on Wednesday, September 19
UK: 18:00 (06:00 PM) on Wednesday, September 19
France: 19:00 (07:00 PM) on Wednesday, September 19
Japan: 02:00 (02:00 AM) on Thursday, September 20
New Zealand: 05:00 (05:00 AM) on Thursday, September 20
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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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The best writing in science papers part 1: Vladimir Nabokov in Notes on Neotropical Plebejinae (Lycaenidae, Lepidoptera)

I have been wanting to start a new series here on my blog about examples of great writing in scientific publications.  There is a lot out there on great science writing.  But that is not what I am writing about here.  I mean actual scientific research papers where the writing itself is exceptional.  And todays example, which may be a bit unfair, comes from the one and only Vladimir Nabokov.  For not only was he a great writer of literature, he was also a lepidopterist.  He was for some time the curator of leps at the Harvard Museum of Comparative Zoology.

I note – I first discovered this when I got a work-study job shelving books at a library at Harvard only to discover that that library had on display a collection of Nabokov’s butterflies.  I got little shelving done when nobody else was around).

Anyway, I had read some of his short stories and book in high school but was not aware of his butterfly obsessions.  What amazed me most was they had some of his butterfly research papers on display too and they were simply amazing to read.  The writing in them is just awesome.

So thus we get to todays’s example of great writing in science papers: Notes on Neotropical Plebejinae (Lycaenidae, Lepidoptera).  Thankfully, somehow, Hindawi publishers have come into possessing of the rights to the back issues of the journal Psyche where this was published and it is freely available as a PDF.  The paper is not perfect mind you – some parts are written more eloquently than others.  But there are sparks in there of what I think are wonderful (for a science research papers).  Some of my favorite parts are quoted below:

The results proved so unexpected and interesting that it seems worth while to publish the present paper despite its rather superficial and incomplete nature.

In a way the initial blunder was Swinhoe’s who while correctly giving a subfamilial ending to the group which Tutt’s intuition and Chapman’s science had recognized (“tribe” Plebeidi which exactly corresponds to the Plebefine of Sternpffer) as different from other “tribes” (i.e., subfamilies) within the Lyccenidce, failed to live up to the generic diagnoses which he simply copied from Chapman’s notes in Tutt and tried to combine genitalic data he had not verified or did not under- stand with the obsolete “naked v. hairy eyes” system (which at Butler’s hands had resulted in probably the most ludicrous assembly of species ever concocted, see for example Butler 1900, Entom. 33: 124), so that in the case of several Indian forms which Chapman had not diagnosed, Swinhoe placed intra-
generically allied species in different subfamilies and species belonging to different Tuttian “tribes” in the same subfamily. [[ YES – THIS IS ONE SENTENCE]]

The arrangement proposed in the present paper needs to be prefaced by a few words on taxonomic units. The strictly biological meaning forcibly attached by some modern zoologists to the specific concept has crippled the latter by removing the morphological moment to a secondary or still more negligible position, while employing terms, e.g., “potential interbreeding,” that might make sense only if an initial morphological approach were presupposed. 

I am sure there are other Nabokov papers with other choice sections … will be looking for those later.  If anyone has suggestions for other great writing in science papers, please post comments ..

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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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