Saturday, November 19, 2011
A day of almost pure joy in #DavisCA and at #UCDavis, until ... #OccupyUCDavis
Well, yesterday seemed to be such a good day at first. In the AM my wife dropped my daughter off at her school (Birch Lane Elementary School famous for the scroll they sent the New York Times earlier in the year) and I stayed at home to watch my son (he does not have school on Friday's). Normally I take my daughter to school by bike but today she wanted mommy to take her.
While watching my son, I had a conference call to "discuss" the education series for PLoS Biology. I put discuss in quotes since I have laryngitis and could not really speak. But Liza Gross signed on to gchat during the call and I sent her messages which she then read to the crowd. While on the phone I posted a few things to twitter too (must multitask):
While watching my son, I had a conference call to "discuss" the education series for PLoS Biology. I put discuss in quotes since I have laryngitis and could not really speak. But Liza Gross signed on to gchat during the call and I sent her messages which she then read to the crowd. While on the phone I posted a few things to twitter too (must multitask):
- Protests again gathering steam on UC Davis campus | Davis Enterprise http://shar.es/ooVG7
- More honors for librarian at Birch Lane Elementary in #DavisCA #MyDaughtersSchool #GoLibrarians http://shar.es/ooVjb
- On conference call discussing PLoS Biology's: Open Education series tho hard to discuss w/ laryngitis http://shar.es/oWsSk
- ALEPDAVO @phylogenomics use your computer! macs can talk what you write remember? there's an option for that I think, although it might just spell
- @ALEPDAVO doing chat with other person on phone ...
- markowenmartin: @phylogenomics I tell students we are shedding microbes in an aerosol. Student made me this last year, in reply. pic.twitter.com/F132xlhA
- @markowenmartin that is awesome
- Cool example of PLoS Biology education papers: Bacterial Pigments as an Untapped Resource in the Classroom and Beyondhttp://shar.es/oWtHN
- Another PLoS Biology education pub: Metagenome Annotation Using a Distributed Grid of Undergraduate Studentshttp://shar.es/oWtxE
- Do you survey biological aerosols? If so – feedback wanted on protocols used http://shar.es/oW7XG #microBEnet
- The Tree of Life: Quick post: Do you survey biological aerosols? If so – feedback wanted on protocols used http://goo.gl/fb/PJ3G6
- Course Announcement: Introduction to Food- and Air-Borne Fungi, June 18-22 Ottawa http://shar.es/oWu4F
Friday, November 18, 2011
Quick post: Do you survey biological aerosols? If so – feedback wanted on protocols used
Please see this post if you sample biological aerosols:
Tuesday, November 15, 2011
Among the strangest official email msgs I have ever received
It has been brought to my attention that the practice of standing on the toilet seat has not only been identified in the women’s restroom, but also the men’s restroom. As a follow-up, the MSO/CAO for the departments has been notified of this safety & sanitary concern. As part of the corrective action, all stall doors (women and men) will be posted with the following notice: FOR SAFETY AND SANITARY REASONS, PLEASE DO NOT STAND ON THE TOILET SEAT.
Monday, November 14, 2011
Seriously annoyed with Nucleic Acids Research and Oxford University Press right now
Well, I was working on adding some paper links for an online version of my CV and I discovered something very annoying.
I went to get a link for my 1994 paper in Nucleic Acids Research. I wrote this paper with my then girlfriend, now wife, and her advisor Ginny Walbot. The paper was on finding a "transpose" motif in one of the proteins that was part of the autonomous element for the Mutator transposon in maize "Sequence similarity of putative transposases links the maize Mutator autonomous element and a group of bacterial insertion sequences."
So I went to Pubmed and searched for Eisen JA and Mutator and got the Pubmed entry here. And then I looked at the links in the upper right and there were two. One to NAR and one to Pubmed Central. I note - the paper has been freely available online for years. I vaguely remembered noticing some issue with the NAR version in the past so I went to that site. And there it was
Wow. Even though the paper is freely available in Pubmed Central, NAR is trying to charge for it.
What the f**#?
Same thing for my other NAR articles:
Not sure what the deal with this is. Could be a glitch. COuld be a feature.
I went to get a link for my 1994 paper in Nucleic Acids Research. I wrote this paper with my then girlfriend, now wife, and her advisor Ginny Walbot. The paper was on finding a "transpose" motif in one of the proteins that was part of the autonomous element for the Mutator transposon in maize "Sequence similarity of putative transposases links the maize Mutator autonomous element and a group of bacterial insertion sequences."
So I went to Pubmed and searched for Eisen JA and Mutator and got the Pubmed entry here. And then I looked at the links in the upper right and there were two. One to NAR and one to Pubmed Central. I note - the paper has been freely available online for years. I vaguely remembered noticing some issue with the NAR version in the past so I went to that site. And there it was
What the f**#?
Same thing for my other NAR articles:
- Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions.
- A phylogenomic study of the MutS family of proteins.
- TIGRFAMs: a protein family resource for the functional identification of proteins.
Not sure what the deal with this is. Could be a glitch. COuld be a feature.
Sunday, November 13, 2011
Friday, November 11, 2011
Top 11 biology things with a connection to 11 for 11:11:11 AM on 11/11/11
In honor of 11:11:11 on 11/11/11
Things about 11 in Biology
Things about 11 in Biology
- Chromosome 11 (human) - Wikipedia, the free encyclopedia
- The spatial-temporal clustering of Plasmodium falciparum infection over eleven years in Gezira State, The Sudan
- Simultaneous Determination of Eleven Major Flavonoids in the Pollen of Typha angustifolia by HPLC-PDA-MS.
- The cell generation cycle of the eleven-day mouse embryo
- Eleven daughters of NANOG.
- RPS11 - Wikipedia, the free encyclopedia
- Development and evolution of a variable left-right asymmetry in nematodes: the handedness of P11/P12 migration.
- Functional display of family 11 endoxylanases on the surface of phage M13.
- Polypeptide synthesis during lytic induction of phage 11 of Staphylococcus aureus.
- Evidence of Infection with H4 and H11 Avian Influenza Viruses among Lebanese Chicken Growers.
- Phylogenetic analysis of avian influenza viruses of H11 subtype isolated in Kazakhstan.
Reading about Medical School requirements -
Just a quick one here. I am reading up on medical school curricula because I am thinking about designing a course on evolutionary medicine. Wondering what is going on these days with modernizing med. school requirements (that is what students need to take before med school) and what they take in med school.
I found this interesting page: Harvard Medical School: Requirements discussing revisions to what Harvard requires for incoming med. school students.
This led me to this HHMI AAM report which has some useful discussion of what physicians should learn about. I was glad to see a bit here and there about evolution. It is even listed as a core competency "Competency E8
Demonstrate an understanding of how the organizing principle of evolution by natural selection explains the diversity of life on earth." with specific examples of things that could be taught.
If anyone knows any other good review docs on med. school requirements or med. school curricula I would appreciate pointers.
Thanks
Thursday, November 10, 2011
Wednesday, November 09, 2011
What you need to know about infectious disease?
New video from Institute of Medicine on "What you need to know about infectious disease" which is useful and fortunately includes some information about things other than infectious diseases.
It is based on this booklet.
It is based on this booklet.
Gorgeous new book on Evolution
Just got a review copy of Evolution by Jean-Baptiste de Panafieu and Patrick Gries
Haven't read it yet but it looks gorgeous
This is a smaller edition of an oversized hardcover published in 2007
Haven't read it yet but it looks gorgeous
This is a smaller edition of an oversized hardcover published in 2007
Yes I like mixing science and art - but "DNA2Art" seems a bit, well, non artsy #visualiztion≠art
Just got this email
I am representing DNA2Art - a start-up working with creating DNA art. DNA2Art just launched a few new products that I would be glad to share as I think they might be of interest.
DNA2Art takes human uniqueness to a whole new level by enabling visualization of one's personal DNA. DNA based art is a great way to show the beauty of your genes.
DNA art is extraordinary because:
Tuesday, November 08, 2011
I am phylogeny obsessed but this is too much to me: phylogeny of cancer subtypes
Just because you have data that could be plugged into a phylogenetic analysis does not mean it makes sense to do so. Case in point - the following paper:
In this paper the authors take gene expression data from various cancer samples/cell lines and then they build phylogenetic trees from the data. See example below:
Figure 2. A phylogeny of acute myeloid leukemia (AML) subtypes. According to the French-American-British (FAB) classification, AML samples are classified into seven different types according to their level of differentiation (see Table 1). Expression data from 362 AML patients and 7 Myelodysplastic Syndrome (MDS-AML) patients is used to construct a phylogeny of these leukemias. We include expression data of human embryonic stem cells (hESCs), CD34+ cells from bone marrow (CD34 BM) and peripheral blood (CD34 PB), and mononuclear cells from bone marrow (BM) and peripheral blood (PB). The differentiation pathway from hESCs to mononuclear cells from peripheral blood is represented in purple, and the common ancestors of subtypes are shown as pink dots. The bootstrap values of branches are indicated by boxed numbers, representing the percentage of bootstrapping trees containing this branch. The ranking of AML subtypes identified by the phylogenetic algorithm corresponds with the differentiation status indicated by the FAB classification. The M6 subtype, represented by only 10 samples in our dataset, has the least stable branch, leading to lower bootstrap values for those branches where it can alternatively be located.
The pictures are pretty. They make some sense biologically. The paper has some very interesting parts and I do not want to suggest that the paper is not useful. But it makes no sense to me to use a phylogenetic approach to analyze this data. Phylogenetic methods are about reconstructing history of evolutionary lineages. They should not be doing that here as far as I can tell since the cancers are from different people with different histories and what they make be looking at is convergent / developmental similarities in the cancer samples. But they are not looking at history per se. And thus it is not appropriate to use algorithms that use phylogenetic methods:
It just makes no sense to me to use a phylogenetic method instead of some sort of clustering method in the step where it says "construct tree" in their flow diagram. Sure phylogenetic methods can make nice pictures. But they should only be used when the underlying data has a history that is reflected in the model/assumptions of the phylogenetic method. I could, for example build a phylogeny of cities based on various metrics. But would that make sense? Most likely not. Don't get confused by the fact that similar things group together in the same part of a phylogenetic tree to thinking that that means that a phylogenetic model is right for your data.
I may be obsessed with phylogeny but that obsession applies to applying phylogenetic methods to data with histories that are approximated by the methods being used ... and this paper seems to not be doing that ...
Hat tip to Eric Lowe, an undergrad in my lab for showing me this paper.
I note - this does not mean that phylogenetic methods cannot be applied to cancer studies. Case in point - this paper:
Estimation of rearrangement phylogeny for cancer genomes by Greenman CD, Pleasance ED, Newman S, Yang F, Fu B, Nik-Zainal S, Jones D, Lau KW, Carter N, Edwards PA, Futreal PA, Stratton MR, Campbell PJ.
In this paper the authors focus on mutations in cancer cells and they use phylogenetic methods to determine the order in which genomic changes happen in these cancer cells. This seems to be an excellent use of phylogenetic / phylogenomic methods.
So - lesson of the day - phylogenetic methods should be used on data with a phylogenetic history. Not so complicated. But pretty important.
Monica Medina from UC Merced coming to #UCDavis Wed 4 PM "Coral holobiont genomics"
This one should be fun:
Dr. Monica Medina (UC Merced)
“Coral holobiont genomics: Insights into the interplay of a host and its diverse microbial assemblage”
Wednesday, November 9, 2011
4:10pm
1022 Life Sciences
See a little about Monica below:
See a recent PLoS One paper from her here:
Monday, November 07, 2011
Sunday, November 06, 2011
Video of my talk from the Compass 2011 meeting in LA on a "Field Guide to Microbes"
My talk from the Compass Summit on the "Dark Matter of Biology"
The Dark Matter of Biology from Compass Summit on FORA.tv
The Dark Matter of Biology from Compass Summit on FORA.tv
Friday, November 04, 2011
Wanted - examples of "everyday" evolution
A colleague is working on an article on examples of rapid evolution in the context of our "everyday" lives (i.e., things people see/encounter frequently). What is needed are good examples, with citations, of recent rapid evolution.
Some candidate examples include
Some candidate examples include
- Artemisinin resistance in malaria: see http://www.nejm.org/doi/full/10.1056/NEJMoa0808859
- Flu evolution and pandemics - many examples from swine flu, etc.
- MRSA evolution - many papers. See for example Evolution of MRSA During Hospital Transmission and Intercontinental Spread. Science, 327 (5964), 469-474
- PCB resistance in fish
- See this recent Economist article.
- Also see Hudson River Fish Evolves to Live With PCBs - NYTimes.com
Wednesday, November 02, 2011
Searching for a "University Librarian" at UC Davis; plus request for reading material on modern library challenges and opportunities
Well, I have trouble saying no. And thus I have a new committee role at UC Davis. I am a member of the University Librarian Recruitment Advisory Committee at UC Davis tasked with coordinating interviews for, well, the University Librarian position which was just advertised (I have reposted the text of the ad below).
I am writing this post for two reasons. First, I want to encourage qualified candidates to apply (and also encourage people to share the posting with qualified candidates). Second, I am requesting help in gathering material for me (and others) to read about new developments in library activities, especially in a University setting. Any good reviews of the challenges facing University libraries as well as any discussions of new opportunities for libraries would be greatly appreciated.
The Job Ad (taken from a PDF and converted to text/html by me)
The University of California, Davis, invites nominations and applications for the position of University Librarian. The campus seeks an innovative and effective leader to serve as its chief strategist and visionary in developing its next- generation library, combining the traditional strengths of a major research library with new information resources and technology programs that enhance its research, teaching and learning activities. The University Librarian provides overall leadership of the UC Davis General Library in support of University research, instruction, patient care, and community outreach and is responsible for transforming the General Library into an Academic Hub that promotes the effective and innovative use of digital information resources in discovery and learning for the future.
The University of California, Davis is a highly selective, research-intensive institution of approximately 32,000 students, including 7,500 graduate and professional students, an annual research budget that exceeds $600 million, a comprehensive health system and 13 specialized research centers. The university offers graduate study and more than 100 undergraduate majors in four colleges and six professional schools. UC Davis is one of the nation's top public research universities and an integral part of the world's pre-eminent public university system, the University of California. For more than 100 years, UC Davis has engaged in teaching, research, and public service that matters to California and transforms the world. The City of Davis, located in in the heart of the Central Valley, in an environmentally aware and socially innovative community of 65,000 people, is close to the state capital and San Francisco Bay area, and is a unique college town where close relationships between the campus and the local community are valued.
The General Library of the University of California, Davis, is a major U.S. academic research library, operating as an integral part of the University while recognizing obligations to a wider public, particularly the people of California. The University Librarian reports to the Provost and Executive Vice Chancellor and serves as a member of the Council of Deans and Vice Chancellors.
The colleges of Agricultural and Environmental Sciences, Biological Sciences, Engineering, and Letters and Science; the schools of Education, Management, Medicine, Nursing, and Veterinary Medicine; and the UC Davis Health System are all served by the UC Davis General Library, both in Davis and in Sacramento. The Library houses comprehensive, world-class agricultural and veterinary medicine collections, especially in viticulture and enology, environmental sciences and ecology, and comparative medicine as well as broadly based humanities, social sciences, and sciences collections. The Special Collections feature a diverse range of topics from agricultural sciences, to Western Americana, to photographs of rural California and Oregon, and a rich University Archives showcasing the campus's 100-year history. The UC Davis General Library is an active contributor to the highly successful University of California collective efforts of campus libraries and the California Digital Library, providing system-wide online services and access to a wealth of books and journals (~33 million titles), electronic journals (~34,400 titles), large digital image and special collections via Calisphere and the Online Archive of California, and over 422 million web sites in the Web Archiving Service.
Already highly ranked among U.S. public universities, UC Davis aspires to raise its profile even further and recognizes the Library as a key contributor to that achievement. The successful candidate will position the UC Davis Library as a leader among research university libraries and introduce new digital programs to enhance the university’s research and teaching activities.
Specific responsibilities of the position include
The University of California, Davis seeks outstanding candidates who have a deep understanding of the challenges and opportunities facing research university libraries, especially those involving new technologies for research and teaching; successful library management experience in a complex higher education setting; extensive experience conducting research on and implementing innovative library-based services in support of a major research university’s mission of teaching, research and public service; demonstrated knowledge of state-of-the-art information technologies and successful implementation of IT-based services; entrepreneurial experience and a record of success obtaining external funding through grants and resource development; strong analytical, interpersonal, oral and written communication, and collaboration skills; commitment to and record of promoting diversity and equal opportunity in the workplace; and the ability to be an effective spokesperson for the UC Davis General Library and a fully contributing member of the UC Davis senior leadership team. A Master of Science in Library and Information Science or other advanced degree is required.
Initial screening of applications will begin immediately and continue until an appointment is made; however, to receive full consideration, applications must be submitted by no later than November 11, 2011. Nominations (including the nominee’s contact information and materials) should be provided to Linda Fairfield at the following address by November 11, 2011:
Linda Fairfield
Senior Management Group Administrator
Human Resources Administration Building
Phone: 530-752-3954
ldfairfield@ucdavis.edu
Application materials should include a letter addressing how the candidate’s experiences match the position requirements, a resume and contact information for at least five references. Submission of materials as PDF attachments is strongly encouraged.
For more information about University of California, Davis, please visit the Web site at
http://www.ucdavis.edu/index.html
I am writing this post for two reasons. First, I want to encourage qualified candidates to apply (and also encourage people to share the posting with qualified candidates). Second, I am requesting help in gathering material for me (and others) to read about new developments in library activities, especially in a University setting. Any good reviews of the challenges facing University libraries as well as any discussions of new opportunities for libraries would be greatly appreciated.
The Job Ad (taken from a PDF and converted to text/html by me)
The University of California, Davis, invites nominations and applications for the position of University Librarian. The campus seeks an innovative and effective leader to serve as its chief strategist and visionary in developing its next- generation library, combining the traditional strengths of a major research library with new information resources and technology programs that enhance its research, teaching and learning activities. The University Librarian provides overall leadership of the UC Davis General Library in support of University research, instruction, patient care, and community outreach and is responsible for transforming the General Library into an Academic Hub that promotes the effective and innovative use of digital information resources in discovery and learning for the future.
The University of California, Davis is a highly selective, research-intensive institution of approximately 32,000 students, including 7,500 graduate and professional students, an annual research budget that exceeds $600 million, a comprehensive health system and 13 specialized research centers. The university offers graduate study and more than 100 undergraduate majors in four colleges and six professional schools. UC Davis is one of the nation's top public research universities and an integral part of the world's pre-eminent public university system, the University of California. For more than 100 years, UC Davis has engaged in teaching, research, and public service that matters to California and transforms the world. The City of Davis, located in in the heart of the Central Valley, in an environmentally aware and socially innovative community of 65,000 people, is close to the state capital and San Francisco Bay area, and is a unique college town where close relationships between the campus and the local community are valued.
The General Library of the University of California, Davis, is a major U.S. academic research library, operating as an integral part of the University while recognizing obligations to a wider public, particularly the people of California. The University Librarian reports to the Provost and Executive Vice Chancellor and serves as a member of the Council of Deans and Vice Chancellors.
The colleges of Agricultural and Environmental Sciences, Biological Sciences, Engineering, and Letters and Science; the schools of Education, Management, Medicine, Nursing, and Veterinary Medicine; and the UC Davis Health System are all served by the UC Davis General Library, both in Davis and in Sacramento. The Library houses comprehensive, world-class agricultural and veterinary medicine collections, especially in viticulture and enology, environmental sciences and ecology, and comparative medicine as well as broadly based humanities, social sciences, and sciences collections. The Special Collections feature a diverse range of topics from agricultural sciences, to Western Americana, to photographs of rural California and Oregon, and a rich University Archives showcasing the campus's 100-year history. The UC Davis General Library is an active contributor to the highly successful University of California collective efforts of campus libraries and the California Digital Library, providing system-wide online services and access to a wealth of books and journals (~33 million titles), electronic journals (~34,400 titles), large digital image and special collections via Calisphere and the Online Archive of California, and over 422 million web sites in the Web Archiving Service.
Already highly ranked among U.S. public universities, UC Davis aspires to raise its profile even further and recognizes the Library as a key contributor to that achievement. The successful candidate will position the UC Davis Library as a leader among research university libraries and introduce new digital programs to enhance the university’s research and teaching activities.
Specific responsibilities of the position include
- Strategic planning for and leadership in development of information resources and related programs and services, both print and digital, in collaboration with other organizations at Davis, across the UC system, and with relevant national and international organizations;
- Development of advanced, innovative e-research and educational technology information and publishing services;
- Oversight of library operations in support of the university’s strategic goals and current research and teaching activities;
- Lead the development of Library digital services, including digital reformatting of existing collections, creation of unique and original digital resources in various formats, and development of web-based interfaces to these resources;
- Leadership of a 120-plus member staff and responsibility for a budget of $24.7M, as well as philanthropic cultivation and stewardship;
- Strategic planning, including long-range planning for service, staffing, automation, and physical facilities to meet the needs of the greatest number of users with an eye to the rapidly evolving patterns of users’ preferred modes of access;
- Representing the library with the UC Davis administrative and academic departments and Davis in UC system- wide discussions, national and international research library and academic technology initiatives.
The University of California, Davis seeks outstanding candidates who have a deep understanding of the challenges and opportunities facing research university libraries, especially those involving new technologies for research and teaching; successful library management experience in a complex higher education setting; extensive experience conducting research on and implementing innovative library-based services in support of a major research university’s mission of teaching, research and public service; demonstrated knowledge of state-of-the-art information technologies and successful implementation of IT-based services; entrepreneurial experience and a record of success obtaining external funding through grants and resource development; strong analytical, interpersonal, oral and written communication, and collaboration skills; commitment to and record of promoting diversity and equal opportunity in the workplace; and the ability to be an effective spokesperson for the UC Davis General Library and a fully contributing member of the UC Davis senior leadership team. A Master of Science in Library and Information Science or other advanced degree is required.
Initial screening of applications will begin immediately and continue until an appointment is made; however, to receive full consideration, applications must be submitted by no later than November 11, 2011. Nominations (including the nominee’s contact information and materials) should be provided to Linda Fairfield at the following address by November 11, 2011:
Linda Fairfield
Senior Management Group Administrator
Human Resources Administration Building
Phone: 530-752-3954
ldfairfield@ucdavis.edu
Application materials should include a letter addressing how the candidate’s experiences match the position requirements, a resume and contact information for at least five references. Submission of materials as PDF attachments is strongly encouraged.
For more information about University of California, Davis, please visit the Web site at
http://www.ucdavis.edu/index.html
Playing with @buzzumi - did a video chat with @betascience discussing metagenomics
Buzzumi looks pretty nice. Was really easy to set up and get running and worked easily for a private video chat. Going to try to use it for a webinar next. Ignore the comments by Russell in the chat ...
Playing with @buzzumi - did a video chat with @betascience discussing metagenomics
Buzzumi looks pretty nice. Was really easy to set up and get running and worked easily for a private video chat. Going to try to use it for a webinar next. Ignore the comments by Russell in the chat ...
Tuesday, November 01, 2011
Evolution pumpkins - from Darwin to Woese
 |
| "I think" in honor of Darwin |
 |
| Woese Tree of Life |
Subscribe to:
Posts (Atom)
Most recent post
A ton to be thankful for -- here is one part of that - all the acknowledgement sections from my scholarly papers
So - it is another Thanksgiving Day and in addition to thinking about family, and football, and Alice's Restaurant, I also think a lot a...
-
Wow. Just wow. And not in a good way. Just got an email invitation to a meeting. The meeting is " THE FIRST ANNUAL WINTER Q-BIO ...
-
Well, I have tried to hold off giving out awards here since I kind of botched my last attempt at this. But here goes. Yesterday, researcher... -
Wow - until I started sniffing around actively, I never realized how much crap was out there in regard to the microbiome. But there is so s...
