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 ..
//player.vimeo.com/video/77610546?title=0&byline=0&portrait=0
RESISTANCE TEASER I from uji films on Vimeo.
I am cross posting this from the UC Davis ADVANCE Blog where I posted it yesterday, since it is of relevance to this project and to the upcoming meeting we are organizing on “Publish or perish? The future of academic publishing and careers.”
There is an interesting new paper in Nature of interest. The paper is titled “Bibliometrics: Global gender disparities in science” and is by Vincent Larivière, Chaoqun Ni, Yves Gingras, Blaise Cronin & Cassidy R. Sugimoto. In the paper the authors report a detailed analysis three parameters:
They then assigned gender to authors using multiple sources and examined the relationships between the 3 listed parameters and gender. And the findings are pretty striking.
I note – it is worth going to the Nature web cite for this article because some of the figures are interactive and one can click on different fields and change the plots.
The authors state – before digging into the details of their analysis “In our view, the scale of this study provides much-needed empirical evidence of the inequality that is still all too pervasive in science. It should serve as a call to action for the development of higher education and science policy.” A pretty strong statement that at least to me seems to be worth considering given their analysis.
Among their findings
The authors then discuss the implications of their findings and make some recommendations for future actions. Among their conclusions (which I quote directly so as to not alter any implied meaning):
This paper is definitely worth looking at in detail. And I note there is also a lot of supplemental material that might be worth downloading and playing around with. Data is critical for understanding the gender disparities in science and for planning and then testing ways to correct such disparities
Erik Kansa has an interesting post directly related to this ICIS project: Digging Digitally » It’s the Neoliberalism, Stupid: Why Open Access / Data / Science is not Enough. In his post Erik discusses some concerns he has with the “Openness” movement. Not that he is against openness – he is one of the biggest supporters of openness out there. But he has concerns with the need to go beyond just making material open. For example he writes
The problem is that the need for reform goes far deeper than simply making papers and data available under CC-By or CC-Zero. Exploitative publishing regimes are symptomatic of larger problems in the distribution of wealth and power. The concentration of wealth that warps so much of our political and economic life will inevitably warp the Open Movement toward unintended and unwanted outcomes.
Furthermore, he argues that we need more non-profit entities dedicated to the public good and leveraging openness. For example he writes.
For every PeerJ or Figshare (and these are ultimately just as dependent on continued public financing of research as any grant-driven project), we also need more innovative organizations like the Internet Archive, wholly dedicated to the public good and not the relentless pressure to commoditize everything (especially their patrons’ privacy).
This is definitely worth a look. And, if you want to hear more from Erik, come to the meeting we are organizing in February where he will be talking and will be on a discussion panel. Meeting registration information is here.
Department of Computer Science Colloquium
System design and data provenance in prospective biospecimen collection and management
Nicholas Anderson
Director of Informatics Research, UCDMC
WHEN:Thu Dec 12, 2013 15:10, 50 minutes
WHERE: 1131 Kemper Hall
HOST: Nina Amenta
http://lymond.cs.ucdavis.edu:8080/seminars?type=1&talkid=297
Access to high quality biospecimens collected from patients requires interaction with a range of clinical and operational systems and roles. The NWBiotrust system implements a modular architecture that encapsulates requirements for security and data use, and tracks the lifecycle of individual patient-acquired biospecimens from collection through processing, clinical annotation and distribution. This system is built to maintain both module and overall workflow auditability of all stages of an implemented study collection protocol. I will discuss the design requirements for this system, and the challenges involved in implementing systems which cross institutional legal privacy boundaries.
PacBio is hosting an evening symposium next week as part of another workshop I’m organizing on campus. All are encouraged to attend! Plenty of food available afterwards.
PacBio Sequence Assembly Workshop
Tuesday, December 17th 2013, 4 pm – 7 pm
The Auditorium, 1005 GBSF
4:00 pm Welcome & Introductions
4:00 – 4:30 pm Shane Brubaker, Solazymes
“Assembly, haplotyping, and annotation of a high GC algal genome.”
4:30 – 5:00 pm Jason Chin, PacBio
“String graph assembly for diploid genomes with long reads.”
5:00 – 5:30 pm Lex Nederbragt, University of Oslo
“Using PacBio reads to improve and validate the assembly of the complex Atlantic cod genome.”
5:30 – 6:00 pm Lawrence Hon, PacBio
“Larger genome hybrid assembly with PacBio.”
6 pm – 7:00 pm Reception & Discussions
Light Refreshments Will Be Served in GBSF Lobby
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.
Image obtained from Cornell News.
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| “Tribal Warfare,” lithography and screen print.by Rebecca Potash. |
“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.”
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.
Department of Microbiology & Molecular Genetics Recruitment Seminar
Kimberley Seed, Ph.D.
(Tufts University School of Medicine)
"Microbial warfare: Evolutionary dynamics between epidemic Vibrio cholerae and a predatory phage"
Monday, December 9, 2013
10:00 am
1022 Life SciencesHost: Prof. Rebecca Parales, Dept. of Microbiology & Molecular Genetics
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Jonathan Eisen's Lab 