Friday, December 13, 2013

Fun to see how Resistance the Film is coming along ... teaser released

Did an interview a while back with Michael Graziano for a film he was working on -- "Resistance the Film" which is coming out soon. They released a trailer for the movie, and it has part of the interview with me as the narration ..

RESISTANCE TEASER I from uji films on Vimeo.

Thursday, December 12, 2013

Wednesday, December 11, 2013

Nice microbe-art-education example from Cornell

Cool story from the Cornell News: Bacteria research inspires students' creative artwork | Cornell Chronicle.  It discusses a course taught by Prof. Greg Page "Introduction to Print Media".  As part of the course the students got a guest lecture from none other than Ruth Ley - who is a faculty member at Cornell and who does some of the most interesting microbiome work around.

Anyway - this guest lecture inspired some of the students in the course to make some microbial themed art works.  And the ones shown on the Cornell News site are wonderful.  Consider this one:
Image obtained from Cornell News.
"Tribal Warfare," lithography and screen Rebecca Potash.
I also love the lines from Ruth Ley on why she got involved in this and what she plans to do in the future.  Consider this:
“As part of my teaching at Cornell, I plan on training science students in the interpretation of concepts in visual arts and eventually even have them learn some basic skills for producing images or video,” Ley said. “I also want to bring science to fine arts students, and my collaboration with Professor Page was my first attempt at this.”
Nice.  Got to try and do more things like this myself ... 

Tuesday, December 10, 2013

Things I don't understand episode 2000: Why in comparing humans & other animals the null hypothesis people always use (and thus try to disprove) is that humans ≠ animals

Well, this is something I just do not understand.  I am sure others out there have thought about this more than I have.  Just read this article: Considering the Humanity of Nonhumans - discussing humans vs. non human animals.  And there is this extensive discussion in there about whether animals have self awareness, and whether they deserve legal rights, and such.  All very interesting I think.

But one part I do not understand.  It is very clear that humans and other animals have many homologous features.  It is very clear that humans are more closely related to some animals (e.g., primates) than to others.  For many comparative studies of animals, if one wants to claim that some animal has a feature that is different from it's close relatives, it is frequently up to the person proposing such a difference to disprove the null hypothesis that the close relatives are the same.  This is the case when studying molecular processes, cell structures, physiology, genome structure, and so on.

Yet, there are a few biological features regarding humans for which it seems the null hypothesis everyone is forced to work with is the reverse.  In these cases the null hypothesis is that we (i.e., humans) are unique and those who wish to claim that humans and other animals are similar / the same have to disprove the null hypothesis.  This seems, well, awkward, at best.  Basically, for some features - especially those that relate to intelligence and behavior  -  if one wants to claim that they are not unique one has to disprove the null.  And yet, for all other features, the null hypothesis is that humans are not unique and those wanting to show uniqueness are forced to disprove this.  On the one hand, I get this.  There are many reasons why one might want to treat "humans are unique" in regards to intelligence and behavior - as the null hypothesis.  But on the other hand - this seems exceptionally anthropocentric and has almost certainly prevented us from discovering and understanding certain behaviors and intelligence-related issues in non human animals.  How do we as a community decided which null hypothesis to use for each phenotype?

Anyway - there it is.  Something I do not understand.

Sunday, December 08, 2013

CVS marketing probiotics for everyone - even kids - & the disclaimers are barely visible

Just got back from the CVS drug store in Davis, CA and thought I would share some of the probiotic promotion they are doing.  Not only are the probiotics now right next to the pharmacy counter (moving up in the world I suppose) but the probiotics are being marketed to all sorts of targeted groups.  Alas, the science behind the claims here are dubious.  And - sadly - CVS makes the disclaimer barely visible in many of the signs.

Wednesday, December 04, 2013

Transitions in the CAMERA metagenomics database ---

Just got this email announcement that I thought would be of interest:

Thank you for being a CAMERA user during its first phases of operation as a
resource for environmental genomics. During the past few years, CAMERA has
been able to offer a number of important community resources, including an
exceptionally well curated environmental genomic database, the ability for
researchers to deposit molecular sequence datasets with associated
environmental parameters (metadata), open access to computational resources
to enable metagenomic comparisons, educational resources and helpdesk
services. These efforts have been funded through the Gordon and Betty Moore
Foundation (GBMF) Marine Microbiology Initiative and the National Science
Foundation to serve the needs of the marine microbiology community and
other users.

As we announced earlier this year, CAMERA is undergoing a transition,
shifting from the Testing and Development phase of CAMERA 2.0 into multiple
entities that are supported by federal and foundation-funded projects for
developing and managing databases. Toward this end, we are re-prioritizing
access to the advanced data analysis capabilities of the system (see below)
while maintaining free and open access to CAMERA’s rich collection of
curated data and metadata. This will involve CAMERA being restructured into
a publicly accessible Data Distribution Center consisting of a simplified
website to enable streamlined access for downloading of sequence datasets
and associated metadata. This new interface will serve as an intuitively
accessible central repository, facilitating direct access to genomic,
metagenomic, transcriptomic, and metatransciptomic projects. Further, the
CAMERA 3.0 database will continue to grow and be maintained with the
inclusion of additional marine microbial datasets, such as the ~700 new
marine microbial eukaryote transcriptome datasets as part of the Marine
Microbial Eukaryote Transcriptome Sequencing Project

In the past, the CAMERA 2.0 compute resources, which include large-scale
BLAST capabilities and other workflow-enabled analysis capabilities, were
generously supported by the GBMF, the San Diego Supercomputer Center, the
NSF XSEDE program, and commercial Cloud computing resource providers,
Amazon and CODONiS. Due to increasing computational costs and the need for
scalability to larger, more complex datasets, it is now necessary for
CAMERA 3.0 to adopt a resource access model wherein projects will need to
identify sources of funding to cover their use of these advanced
capabilities. Starting January 1, 2014, CAMERA 3.0 will no longer offer the
use of computational resources to projects that cannot identify a source of
support for this component of CAMERA 3.0 services. As we shift to this new
usage model, we urge current users to download and save customized data
cart holdings and workflow analysis results before January 1, 2014.

While we are shifting to a restricted resource compute model, we will
continue to improve the capabilities of the system to expand the scientific
breadth of the data managed by CAMERA 3.0. For example, CAMERA 3.0 includes
fully functioning workflows for Illumina datasets, which can be made
available to those users who can identify a source of support for the
associated computational costs. In addition, CAMERA is actively seeking
resources to continue to take community data submissions. If you are now
collecting or have plans to collect data which you wish to deposit in
CAMERA, we urge you to contact us to help you to determine how to obtain
the resources required for these data to be archived and made available
through CAMERA.

Tuesday, December 03, 2013

Hope from sadness: Loreto Godoy Memorial Fellowship (needs $5K more to become permanently endowed)

I received tonight an email from Dr. Holly Ernest, a colleague of mine who is a Professor at UC Davis and I am posting it below. The email relates to a fundraiser for a Memorial Fellowship in honor of Loreto Godoy who was a PhD student here at UC Davis in the Graduate Group in Ecology.  She tragically died this summer in a car crash that also took the life of her husband's parents.  The email relates to a fund that was established in her honor - which needs only an additional $5000 to become a permanently endowed fund at UC Davis.  Holly Ernest was her PhD Advisor and I encourage everyone to read the email below and consider donating to the fund.  Life is so incredibly tragic sometimes.  Loreto was not just a brilliant scientist, but also a wonderful person and a mother of two young girls.  But hopefully through this fellowship some good things can happen for others and her memory can live on.

Dear Ecology community,

Our dreams for a permanently endowed Loreto Godoy Memorial Fellowship are nearly realized.

This fellowship is intended to be awarded regularly to UC Davis graduate students who exemplify Loreto's ideals. Loreto was a PhD candidate in the Ecology Graduate group, brilliant scientist, a loving mother of two little girls, Chilean, veterinarian, and all-around wonderful sunny person.

In order to help us reach our goal of endowing the fellowship and having a lasting legacy of Loreto's wonderful and generous life, my husband Bruce and I are making another gift of $1000 to help inspire others to donate (any size donation is very welcome).

With this donation and that of a new anonymous donor, the fund is now at $20,000. It needs to reach $25,000 to be permanently endowed by UC Davis for a lasting legacy to Loreto's memory.

Please consider joining us to reach this goal!

Also - please feel free to share this email so that others can get involved.

Please send checks to the following address, and write, "for Loreto Godoy Fellowship Fund" in subject line of check:

University of California, Davis
Janet Berry—University Development
UC Davis Conference Center, 2nd floor
One Shields Ave.
Davis, CA 95616-5270

Questions can be directed to Janet by email or phone (530) 902-1624. If you prefer to pay by credit card, you may also call Janet at this number in order to provide this information.

Thank you,

Sincerely Holly Ernest
Loreto's graduate school adviser

(Note by Jonathan Eisen - donations can also be made via the online site 

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