Is collecting specimens necessary?

Feed: iPhylo

Some interesting threads in TAXACOM today (yes, really). The following article has appeared in Science:Minteer, B. A., Collins, J. P., Love, K. E., & Puschendorf, R. (2014, April 18). Avoiding (Re)extinction. Science. American Association for the Advancement of Science (AAAS).

Global Engage Plant Genomics Meeting - Bring Your Y Chromosome Because they Don't Take XX - Calling for a Boycott of this Group

Feed: The Tree of Life

Saw this tweet earlier todayNot one woman: WTF— Female Scientist (@female_science) April 16, 2014And something seemed hauntingly familiar about the organization referenced.  Turns out this is not the first time they have had issues with Gender Balance.  So I respondedWell @female_science Global Engage does it again - I posted about their previous meeting gender ratio issues here— Jonathan Eisen (@phylogenomics) April 16, 2014Incredibly distasteful and painful to see this.

Breaking the Biodiversity Heritage Library

Feed: iPhylo

The Biodiversity Heritage Library (BHL) has recently introduced a feature that I strongly dislike. The post describing this feature (Inspiring discovery through free access to biodiversity knowledge... states:Now BHL is expanding the data model for its portal to be able to accommodate references to content in other well-known repositories.

Now accepting submissions through Facebook

Feed: Carnival of Evolution: The Best of Evolutionary Blogging of the Last Month continues to be down, so I am hereby officially discontinuing the use of it for submissions to CoE. Instead, people are encouraged to submit via the Facebook page CarnyEvolution.The next host will be listed with links to their blog and a Twitter handle, if they have one.

We have a host for May 1st CoE

Feed: Carnival of Evolution: The Best of Evolutionary Blogging of the Last Month

E. E. Giorgi is hosting the next Carnival of Evolution at Chimeras.You can submit posts on evolution (even ones you didn't write) by linking to them in the comments here.

And let the microbiology word play begin (re Entamoeba feeding)

Feed: The Tree of Life

New paper out about feeding by the parasitic amoeba Entamoeba histolytica.  Apparently, the work shows that this organism feeds by in essence taking bites out of cells.  (I say apparently because the paper is not open access and I don't have access to it from where I am writing).Anyway - there are a lot of news stories about this.  And for some reason (I am not quite sure why) this has inspired headline writers to get out their pun pens and creative thinking caps.

User interface to edit a point location

Feed: iPhylo

CircleFollowing on from earlier posts on annotating biodiversity data (Rethinking annotating biodiversity data and More on annotating biodiversity data: beyond sticky notes and wikis) I've started playing with user interfaces for editing data. For example, here's a simple interface to edit the location of a specimen or observation (inspired by the iNaturalist observation editor).

And in non shocking news of the day - more overselling of the microbiome

Feed: The Tree of Life

Well, just read this story: Possible link between bacteria and breast cancer: study | CTV London News.  Serious overselling of the microbiome going on here.  As far as I can tell, all that was shown in the work discussed here (for which there is no publication or presentation of any kind reported) is that the bacteria found in canecrous breast tissue differs from that in non cancerous tissue.  Interesting perhaps.  But not really that informative as just about every time anyone has ever looked at two samples from patients with different health conditions, the microbiome is different.

Guest post by Kevin Penn: In Search of Bacteria on Drugs: Secondary Metabolites and Microbial Ecology

Feed: The Tree of Life

Below is a guest post from Kevin Penn, who used to work in my lab ...I am a former Research Associate of Jonathan’s interested in understanding evolution and ecology of microbes in natural environments.  Recently I’ve become interested in learning about the expression of secondary metabolite related genes in natural settings to put the gene’s products into an ecological context, because almost certainly microbes are not making natural products just to benefit humans.

The Experimenter’s Museum: GenBank, Natural History, and the Moral Economies of Biomedicine

Feed: iPhylo

An undergraduate student (Aime Rankin) doing a project with me on citation and impact of museum collections came across a paper I hadn't seen before:Strasser, B. J. (2011, March). The Experimenter’s Museum: GenBank, Natural History, and the Moral Economies of Biomedicine. Isis. University of Chicago Press. doi:10.1086/658657Unfortunately the paper is behind a paywall, but here's the abstract (you can also get a PDF here):Today, the production of knowledge in the experimental life sciences relies crucially on the use of biological data collections, such as DNA sequence databases.

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