Tag: Misc.

New undergraduate research project: Aquarium Biogeography

Last year we undertook an undergraduate research program to isolate bacteria and sequence reference genomes from the built environment.  That work is still ongoing, and can be found here.

 
This year we’re going to take a look at the biogeography and succession of microbial communities in aquariums.  We’re fortunate to have access to several aquariums here on campus that we can examine.  We’ll be looking at a number of different questions, more detail will be forthcoming in student posts.

 
We had our first meeting yesterday and will begin sampling aquariums starting this coming Monday.  Watch this space for information on our progress.

Safety Reminders in the Research Lab

Am posting this to the lab blog because it seemed pretty important to share as broadly as possible. Safety first.

Safety Reminders in a Research Laboratory.pdf

Some arguments for why Carl Woese (and probably Norm Pace) deserves a Nobel Prize

Compiling posts and articles discussing why Carl Woese deserves a Nobel Prize.  Will be writing a new article on this but felt like I should share the articles in case I don’t get done in time

I note I do not think Woese should win a Nobel for discovering the archaea.  That was a groundbreaking finding but it does not fit well with the Nobel Prize categories.  I think he should win it for the concept of molecular classification of microorganisms and applying this in general to the microbial world around us.  This concept (expanded by Norm Pace and colleagues to uncultured microbes) revolutionized our approach to studying single microbes in the environment, to studying single microbes infecting people and to studying communities of microbes in and on people.  And thus Woese and Pace in my opinion deserve the Nobel Prize for Medicine.  I will be expanding on this in a future post …
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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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American Chemical Society not winning any blogging friends these days

Wow – just got an email from a colleague with details on a scientific publishing saga.  Here is the summary:

Stage 1: Jenica Rogers wrote a blog post expressing a bit of frustration with the American Chemical Society and their publishing system: Walking away from the American Chemical Society

Stage 2: The Chronicle for Higher Education wrote a story about it: As Chemistry Journals’ Prices Rise, A Librarian Just Says No

Stage 3: The Director of Public Affairs for the ACS responded to questions and was quoted with the following

“We find little constructive dialogue can be had on blogs and other listservs where logic, balance and common courtesy are not practiced and observed,” Glenn S. Ruskin, the group’s director of public affairs, said in an e-mail message. “As a matter of practice, ACS finds that direct engagement via telephone or face-to-face with individuals expressing concern over pricing or other related matters is the most productive means to finding common ground and resolution.”

Then he attempted to clarify some details of the quote in that he claimed that the following got left off the end of the quote “Therefore, we will not be offering any response  to this blog posting or the conversation that has ensued.” but when doing this he got a bit personal and nasty:

The individual responsible for the above cited blog certainly has the right to her opinion, but that does not excuse rude behavior or her use of profanity and vulgarity in addressing ACS or its employees. While not evident in the most recent postings, I won’t repeat what she has posted in the past.  But I think you would agree that vulgarity and profanity postings do not lend themselves to meaningful, productive and civil discourse, thus our decision not to engage any further with her on this topic

And the discussion continued on various blogs like Chembark.  The most disturbing part to me of the whole thing is that it is hard to find anything particularly extremely vulgar in writings by Jenica Rogers (I note – I only googled around for a minute or so so I may have missed things but Walk Walt at Random has more detail on this and also did not find any serious vulgarity).  Generally I find the response of ACS to be extremely distasteful.  They don’t like what she wrote.  So they go after her character.  Brilliant.

For other takes on this story 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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Headline says it all "Opera singer grows algae on her face by feeding it w/ her breath & then the audience eats it"

Wow.  I am always on the lookout for microbe-themed art.  In most cases, when I see such art, I think “wow – that is an interesting way of embedding microbes into a traditional form of art”.  You know – painting with microbes or art with microbes in it or such.  Well, in this new case I can say this is the most unusual and most creative use of microbes in art I have ever seen: Opera singer grows algae on her face by feeding it with her breath and then the audience eats it

You see, an opera singer work a “head-mounted, face-clinging device” which contained within in some algae in water.  And then the algae was fed by the opera singer’s breath.  This is part of something called the “Algae Opera“.  The most amazing part of this is described in the io9 article

“Because the algae’s growth is dependant on the amount of CO2 it receives, the singer controlled her pitch and volume to alter various characteristics of the algae, including taste (what they called “sonic enhancement”). Depending on the way she sang, the different pitches and frequencies could make the food taste either bitter or sweet”

And then at the end of the performances the audience was invited to sample some of the algae. Yum.  Certainly a bit weird.  But kudos on the creativity index.

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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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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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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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