Author: Jonathan Eisen

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 – NYTimes.com 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.

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
(marinemicroeukaryotes.org).

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.