Monte Bloggo

Grad student blogging/ academic life (Amber, Ania)

2009-03-08T16:55:00.000-07:00

We looked at two graduate student blogs and one post-doc blog that discuss the mentor-mentee relationship and the disjoint between what is expected of both parties and what ends up being supported.
The blogger at ilovescience points out that what students may be encouraged to do theoretically (attending training seminars, TA training, etc) may not be what is supported in reality.
Wecansleeplater does a CBA on the mentor-mentee relationship. One point that stuck out to me was that from a purely CBA standpoint, the PI should only be invested in what happens to the student while they are currently a member of the lab. This may be why there is such a precipitous drop off of women in science after graduate school. There is little support or information available for women who wish to pursue a career and develop of a family.
Far more radical, YoungFemaleScientist, a post-doctoral researcher, rails against the sexism she perceives in the mentor-mentee relationship and follows up the comments here. I feel that there may be some truth to what she says, however, I'm not sure how much of what she is writing is colored more by poor mentor-mentee relationships that have nothing to do with gender.
Female Science Professor does dole out "street smarts" in her post on academic etiquette to both males and females who read her blog. These unwritten rules, most of which are common sense, are crucial. What would you add?

Science Tools 2.0

2009-03-01T11:42:00.000-08:00

This week’s topic is “other web 2.0 applications”. In my opinion, this is one of the more exciting developments at the interface between science and technology over the last 5 years or so, it's also rapidly changing. The major themes in this area (as I see them) are:

- increasing integration between data sources and/or analysis strategies
- accessibility and low learning curves
- resource availability

In some cases, this simply amounts to using standard web 2.0 tools (e.g., wikis and blogs) in order to organize and present scientific information in useful ways, in other cases these tools are novel applications developed with a specific purpose in mind. I’ve linked to some resources that I’ve found useful or think are cool. This list is heavily biased toward the type of resources that I use most (phylogenetics and biodiversity informatics), feel free to add others in the comments.

Increasing integration
GBIF - Global Biodiversity Information Facility
Genbank
Scratchpads - Customizable collaboration for taxonomic research
Phylota - Mike Sanderson's database that packages genbank into phylogenetically useful clusters
dryad - Nescent funded data repository

Accessibility
Tree tapper - Former CPBer Brian O'Meara's Nescent postodoctoral project.
Phylowiki - phylogenetics tutorials as a wiki, developed as part of the Bodega Applied Phylogenetics Course
OpenWetWare - lab notebooks, blogs, protocols, etc.
BEAST user guide - example of using a wiki to develop a user guide to complicated software
Cipres - popular phylogenetic inference methods made easy
iTOL - tree visualization
automated tree inference - mor (rDNA fungal phylogeny), MatriPhy (my package, still in development, link goes to turtle example)

Resource availability
Genome browsers
RDP -ribosomal database
Treebase - database of phylogenies
uBIO - database of taxonomic information
Museum collections: specimens - MaNIS, ORNIS, HerpNET; fieldnotes
EoL - Encyclopedia of Life
Biodiversity heritage library - an effort to digitize all the biodiversity literature in 10 natural history museum libraries
Cipres - Free access to some computing resources at the San Diego Supercomputer Center

One could also argue that new online “rapid publication” journals are part of this trend (E.g. Zootaxa, Zookeys, PLoS one). I’ve only had one experience with this type of journal to date and found it to be really great for certain types of papers, I’d be interested to hear about other’s experiences.

In many ways, science is only beginning to take advantage of web 2.0 technologies and I think most would agree that there is a lot of potential for more development in this area. Aside from discussing the utility and the impact that these tools have had on science already, I would also be interested in discussing what resources people think are currently missing and what future developers should be aiming for.

Nature Editorial on Blogging

2009-02-25T12:55:00.000-08:00

Check out the editorial appearing in this week's Nature, discussing blogging about articles before they are published. Take home message -- go ahead, but watch don't give away too much...
Then go and engage in the discussion on Nature's forum. Guess since this a blog post and not the mass email I had started, I better go share an opinion. Sounds like Nature is taking a cautious approach to authors engaging in blogging -- they talk about the advantage of all work being peer reviewed before being public, but the embargo goes beyond the point when it has been peer reviewed and accepted, but still not published. The justification for this is unclear.

Post Made on Behalf of Clarissa

2009-02-21T13:00:00.000-08:00

Blogs as an Outreach Tool

So there are so many different types of outreach, I thought maybe we could focus on either of the following:

1) Blogs as a medium to communicate science painlessly to the public.

- Here’s an extension of what we talked about last week, a blog for biology teachers: http://blogging4biology.edublogs.org/

- A blogger who interviews scientist doing outreach as her form of outreach:

http://jendodd.com/index.php?option=com_content&view=article&id=67:interview-with-eva-amsen&catid=42:science-outreach&Itemid=54

- And a page of web resources for communicating science effectively to the public:

http://opa.faseb.org/pages/PolicyIssues/commscience.htm

2) Blogs as a yet another tool to reach out to those anti-evolutionist folks (or for them to reach out to us!).

- One interesting thing you find with these types of blogs is often very short posts followed by extended comments. Check out the following three links for examples:

http://www.bbc.co.uk/blogs/thereporters/justinwebb/2009/02/evolution_vs_creationism.html

http://blog.news-record.com/opinion/letters/archives/2008/05/most_true_scientists_do_suppor.shtml

http://firstread.msnbc.msn.com/archive/2009/02/12/1791814.aspx

Framing Science (http://scienceblogs.com/framing-science/ ) is an interesting blog I found that has commented on both of the above and uses the blog as a media tool to connect science with politics.

Education and technology

2009-02-16T21:22:00.000-08:00

I came across this video of Sir Ken Robinson talking at the TED (Technology, Entertainment, Design) Conference in 2006 about our current education system and the effects he thinks it has on kids' creativity. Even though he is talking about lower education, I think his views are relevant to college- or graduate-level science teaching because it is at this point that students are challenged (often for the first time) to think independently and creatively about scientific ideas.

How do we plan to evaluate students in our classrooms while also fostering creativity? If anyone has good ideas about how they plan to do this or good stories about how their professors did this in the past, please share!

I am really interested in how technology can be utilized in the classroom, especially in the context of a college-level biology class. And I'm talking something other than powerpoint presentations, people. Here's an example of a class blog , made by Darren Kuropatwa, a high school math teacher in Manitoba. After each class, he has one student summarize what they learned that day and post it on the blog. He has gotten a lot of good feedback from students who benefited from reading other students' explanations of math concepts. I wonder how a similar blog could work in a college-level biology class? How would you change his model?

Finally, here's the Online Education Database's collection of their top 100 education blogs .

2009-02-09T18:52:00.000-08:00

What Every Scientist Should Know About Open Access

Let's start by learning a little more about the Creative Commons license such as used by PLoS. To do so, we'll include a piece of media licensed under Creative Commons attribution (by) license.

We better attribute it: From Creative Commons, http://creativecommons.org/videos, found on Wikipedia, which is itself becoming Creative Commons (cc-by-sa: attribution and share alike), though currently GFDL. Okay, on to Open Access.

Green and Gold OA
Their are two basic paths to Open Access: the Green road and the Golden road. In Green Open Access, authors self-archive papers. Archiving post-publication is subject to copyright, while as pre-publication is simply a matter of journal policy. Most journals now allow pre-publication archiving -- Nature recently changed their policy to allow this. A long standing example in the physical sciences is arXiv.
Gold Open Access is the PLoS model, where researchers pay $1000 - $3000 to cover publication costs. Many journals use a hybrid model, where the authors have the option to pay and have their paper published as open access, see this list of journals accepting so called "sponsored articles" through Elsiver.

How big is Open Access?
Good question. NIH funded research requires it, as does Harvard.

Think bigger
Need More Openess? How about Open Peer Review? Check out Biology-direct, an open-source, open peer-review model. Authors solicit reviews from three board members and then can be published with or without revisions but with the reviewers comments and names included. Further alternative is Open Peer Commentary, where peer commentary on a target published article is published along with the author's response.

A natural extension of open publication is Open Text Books. Hear Richard Baraniuk discuss on TED talks, which use the cc-by-nd-nc (attribution, non-derivative, non-commercial):

How about all of science being open? Open Data and Open Notebooks? Check out the vision of Science Commons, and the example of Neurocommons.

Blogspot rules and copyright

2009-02-03T12:42:00.000-08:00

Curious about what we are allowed to post on blogger?
the Blogspot Content Policy

Guidelines for copyright infringement, through Google

2009-02-03T12:24:00.000-08:00

Intellectual property/copyright - here's a link explaining the Creative Commons license options (Creative Commons is what PLOS uses, specifically, the Attribution License), a simple way to share and protect your work.

Blogging just feels weird.

2009-01-27T23:21:00.000-08:00

I'd started writing a post about this educational physics blog. I just came across it and it struck me as cute and also relevant to some of the things we've been talking about. Things I would have no problem opening my big mouth about in our class. But I deleted it because it felt totally lame to post it. Even if just to you guys. Even if the next time I saw you I could have very easily and naturally sucked you into a convo about how one would model the decrease in volume of a beer's head over time. I guess I do have an issue with the medium just like GradStudentWithUniqueName was talking about.

My current thinking is that science blogs (and I'm talking independent blogs by active research scientists) are a labor of love expressing a particular strain of science geekery. Of course we are all huge geeks for science, but for some the blog (however you want to define it) is going to be a natural extension of that geekiness and others (most?) not.

Posting this post actually feels just as weird as the last (aborted) one. It's like posting it makes it seem more important than I actually think it is. Two of your minutes in the hallway? No problem. Two of your minutes online? The nerve!

Interesting post

2009-01-27T08:06:00.001-08:00

I just found a blog post that applies to some past conversations (why blog?) and pertains to today's topic (types of blogs). Check it out:

http://scienceblogs.com/bioephemera/2008/09/will_blogs_reshape_the_scienti.php

(Note: Apparently I am too dumb to know how to make this actually link to the page, so you will have to copy and paste the url if you are interested in checking it out...argh)

Types of Blogs

2009-01-23T14:36:00.000-08:00

Hello all,

The topic we will be discussing next week is "Types of Blogs". After reading through the Wikipedia page on blogs, it seems to me that in terms of structure, the two main types of blogs that currently exist are the "common" blogs (which primarily use text, but some may also use other types of media, e.g. photoblogs, videoblogs "vlogs") and "micro-blogs". If you, like me, sort of know something called Twitter exists but don't really use it, check out this vlog to see what all the hype is about (note: I liked the graph at 00:45).

Since I don't think we can spend 50 mins just talking about how blogs use different software or media types etc., I thought it would be appropriate to use part of next week's session as a brief introduction to different types of contents in science blogs, which we will be discussing in the upcoming weeks.

Research-related
Research Blogging
EEB & Flow
Live-blogging: Phoenix Mars Mission

Academic Life
Dr. Jekyll and Mrs. Hyde
Female Science Professor

Education/Outreach
The Last Word (Question Blogging)
Tree Hugger
Shifting Baselines
and just for kicks, here's the link to Discovery Institute's "Evolution News & Views" (non-science [nonsense??]) blog

For all the blogs hyperlinked above, you don't have to focus on the details of the posts (unless you are very intrigued by the contents, of course), but think about the aims that the authors may want to achieve through blogging, and whether blogs are effective media to achieve those aims.

See you all on Tuesday!

EvolDir RSS

2009-01-21T08:36:00.001-08:00

Has anyone else always wished that EvolDir was available as an RSS feed? It is now.

Many thanks to Rod Page!

http://iphylo.blogspot.com/2009/01/darwin-on-twitter.html

Who Blogs and Why?

2009-01-16T18:56:00.001-08:00

Why Microbiologists Blog This is a ten minute video in which a handful of science bloggers describe their blogs, why they blog, and (for some reason) what they think has been the greatest recent advance in Microbiology. Plus, there's that "bacteria" song. Ha!

Here are some posts from a diversity of bloggers in which they talk about why they blog (or in the case of evolgen, why not):
The Ed Techie
Dr. Jekyll & Mrs. Hyde
ScienceRoll
FemaleScienceProfessor
Humans in Science
Intute: Social Sciences Blog
Mixing Memory
The Atlantic
redcatco
bayblab
evolgen

blog on recent advances in ecology and evolutionary ecology

2009-01-15T16:58:00.000-08:00

I just saw this email on Ecolog which may be of interest to our group.

Hi all,

I just wanted to let folks know that I, along with some colleagues have
started an ecology blog called The EEB and Flow (http://evol-eco.blogspot.com/

)

The EEB and Flow was started because, while there are some great science
blogs dedicated to evolution there is conspicuously little blogging of
recent advances in ecology and evolutionary ecology. The posts on this
blog will include highlights of recent exciting papers, thoughts about
the field of ecology and what it means to be an ecologist, spotlight
researchers and their recent work and discussion of applied and
conservation issues. Contributors include a diverse group of junior
researchers representing several nationalities and research interests. And more will be added soon.

We hope this blog will be useful to an array of people. Most
importantly, that the blog is a resource where researchers will can get updated on recent papers outside their immediate area of interest. We hope that graduate students, course instructors and science writers will use this site as a source for learning about what exciting work is being done and about the people doing it.

Feel free to send us comments or to comment directly on the blog.

Sincerely,

Marc Cadotte

http://evol-eco.blogspot.com/

Quarter Schedule

2009-01-14T08:46:00.000-08:00

Here is the schedule and list of topics for the rest of the quarter:

Jan 20: Why blog? Who blogs? (Dena, Jenna)
Jan 27: Types of blogs (Evelyne)
Feb 3: Issues concerning blogging ethics and etiquette, intellectual property and anonymity (Pat)
Feb 10: Publications/ Open science (Carl, Dan)
Feb 17: Blogs used in education (Sarah)
Feb 24: Blogs as an outreach tool (Clarissa, Will)
March 3: Grad student blogging/ academic life (Amber, Ania)
March 10: Other Web 2.0 applications (Bob)

We agreed that links to blogs of interest or other resources should be posted by the end of the day on Friday (the week before you are scheduled to lead the discussion). See you all next week!

Blogs are lurking where you least expect them

2009-01-13T19:57:00.000-08:00

Thanks to our discussion today, I realized that a lot of websites I visit are actually blogs. I hadn't really thought about it before, but once I realized 538 was a blog (by realize, I guess I mean "once Amber told me..."), a whole new world opened up.
None of them are science blogs, but I'm beginning to think that blogs have become so ubiquitous and come so far from the stiff formatting that people don't really realize that they're reading blogs. I think this could be a little dangerous. If you don't know what you're reading, you can't bring the appropriate amount of skepticism to the reading.
On the other hand, looking at pretty dresses or cake disasters does not require a lot of skepticism.

Best Writing on Science Blogs 2008

2009-01-10T22:14:00.000-08:00

The Open Laboratory has put up links to the top ~50 blog posts from science blogs from the last year.

http://scienceblogs.com/clock/2009/01/the_open_laboratory_2008_and_t.php

Best Science Blogs of 2008

2009-01-08T12:52:00.000-08:00

Top 10 finalists for Best Science Blog of 2008 are up at

http://2008.weblogawards.org/polls/best-science-blog/

(links to blogs below the poll)