Catherine Burke, from the University of Technology, Sydney will be presenting during our lab meeting this week.
We will be meeting from 1:30pm to 3:30pm at the Genome Center in room 4202.
Eisen Lab Blog
Lake Arrowhead Microbial Genomes Meeting 2012 Speaker Gender Ratio #LAMG12
- Jeffrey H. Miller
- Jonathan Eisen
- Ashlee Earl
- Lisa Raleigh
- Jonathan Eisen
- Nina R. Salama
- Frederic Bushman
- Kristine Wylie
- Janet K. Jansson
- Forrest Rohwer
- Curtis Huttenhower
- Tanja Woyke
- Maomeng Tong
- Jeffrey Cox
- Susannah Tringe
- Julian Parkhill
- Rustem F. Ismagilov
- Gautam Dantas
- Pamela Yeh
- Mike Gilmore
- Lance B. Price
- James Meadow
- Jason E. Stajich
- Laura Sauder
- Tara Schwartz
- Susanna Remold
- Bernhard Palsson
- Anca Segall
- Trent Northern
- Rick Morgan
- Beth Shank
- Morgan Langille (added)
- Anthony Fodor (added)
- Peter Karp
- Tatiana Tatusova
- Timothy Harkins
- Katrine Whiteson
- Mallory Embree
- Varum Mazumdar
- Abigail McGuire
- Ee-Been Goh
- Shota Atsumi
- Howard Xu
So 37 39 speakers, 16 of which are women. So that comes to 43.2 41%.
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]
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
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.
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:
- Bacteriograph: Photographs Printed with Bacterial Growth
- Zachary Copfer Blends Bacteria And Photography In Bacteriography …
- These Incredible/Gross Photos Were Printed With E. Coli Bacteria
- Here’s one I’ve grown earlier: Scientist-turned-artist uses bacteria to ..
- “Bacteriografia”: artista cria retratos de cientistas famosos utilizando …
Upcoming on phyloseminar "Inferring macroevolutionary processes based on phylogenetic trees"
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 ..
Microbes and hyenas and smells
So when this press release about microbes and hyenas came out: Microbes help hyenas communicate via scent I wanted to write about it. But I could not figure out what I thought about the story. Still don’t know what I think but it is interesting and worth sharing. Also see the original paper:
Kevin R. Theis, Thomas M. Schmidt, Kay E. Holekamp. Evidence for a bacterial mechanism for group-specific social odors among hyenas. Scientific Reports, 2012; 2 DOI: 10.1038/srep00615
For some possible related papers see
- Bats, bacteria, and bat smell: sex-specific diversity of microbes in a sexually selected scent organ
- Problems Caused by Microbes and Treatment Strategies Health and Safety Issues from the Production of Hydrogen Sulphide
- The relationship between oral malodor and volatile sulfur compound–producing bacteria
- Assessing the relationship between concentrations of malodor compounds and odor scores from judges
- Association of odor from infected root canal analyzed by an electronic nose with isolated bacteria
A must read for those interested in "Spin" of science by press releases & in papers
A new paper in PLoS Medicine is of great interest to me: PLOS Medicine: Misrepresentation of Randomized Controlled Trials in Press Releases and News Coverage: A Cohort Study. Bad press releases drive me crazy. And it has been shown that press releases can frequently be a source of scientific misinformation in the press. Interestingly this paper concludes that spin in the papers themselves is correlated to spin in press releases … So in other words, the scientists are partly to blame … Not shocking but interesting …
Quick post: nice #openaccess review: Insights from Genomics into Bacterial Pathogen Populations
Just a quick post here. There is a new review/commentary that may be of interest: PLOS Pathogens: Insights from Genomics into Bacterial Pathogen Populations. By Daniel Wilson from the Wellcome Trust Centre at Oxford.
Full citation: Wilson DJ (2012) Insights from Genomics into Bacterial Pathogen Populations. PLoS Pathog 8(9): e1002874. doi:10.1371/journal.ppat.1002874
It is a nice and useful review …





