Heh. So after I wrote my previous post, I noticed a comment in my spam filter.

[...] This post was mentioned on Twitter by link2peer, SFSU Sch. of Nursing. SFSU Sch. of Nursing said: Have to check out the sites mentioned here. http://is.gd/5WDXY I wonder if any would benefit nursing researchers.

A few of my posts have been retweeted. I had no idea (waving at the twitter folks). Congratulations. You’ve convinced me. I think I’ll give twitter a try. If I consider it a communication tool, a way to disseminate information about my science to a broader audience, then I can see the potential benefits.

I think scientists should embrace using the Internet to connect with each other and to advance career goals and technical aspects. There are many exciting possibilities, especially for scientists….” — Jonathan Weissman in “Should you be Tweeting”, Bonetta (2009).

photo credit: ahisgett

Here’s a list of 600 scientwists (coined by science writer David Bradley of Science Base) if, like me, you’re looking for other scientists to follow.
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Bonetta L (2009). Should you be tweeting? Cell, 139 (3), 452-3 PMID: 19879830

I’ve had this post percolating in draft form for a while, as I come across more web-based resources for scientists.  Yesterday, I saw an article in Cell by Laura Bonetta titled “Should You be Tweeting?”  (OK, I downloaded the pdf of the article from my university library.  I haven’t touched a physical journal, except the ones I receive as part of my membership in professional societies, in years.)  Bonetta discusses how scientists are using the 140 character social networking site, and it’s limitations. Some tweet links to new research, while others feel it provides insufficient space for scientific conversation.

I’ve been torn about tweeting. My hubby, the computer geek, got an account a couple of years ago but rarely uses it.  He gets a real thrill out of trying new technologies, whereas I prefer to understand their utility before signing up.  Twitter, in particular, seemed like so much navel-gazing to me, especially with all the celebrity accounts.

There have been several web services launched in the last few years aimed specifically at the science community, however. I’ve experimented with some of them, and wanted to provide links to these resources for others.

Social Networking for Scientists:

• Graduate Junction – Billed as “The Academic Network for all early career researchers”, Graduate Junction is geared toward graduate level and postdoctoral academics.  Users create a profile, basically an online CV, covering all relevant academic experience. You can search for others with similar interests and create “research links,” your virtual research network, connecting you with potential collaborators around the world.  There are groups organized around various topics, like bioinformatics and evolutionary genetics. The site also has advice forums covering topics from writing your thesis and work/life balance to giving talks and postgraduate jobs.  They are also sponsoring an online poster competition, and are developing a searchable conference database.  Overall, a nice resource for those beginning a career in research. Registration required but free.
• ResearchGate – The “leading professional network for scientists.” Like Graduate Junction, users have a profile, there are groups, and the ability to network with other researchers.  But ResearchGate goes a step further, allowing self-archiving of your publications and providing abstract search functionality, so others can read about your research and you can search for connections via their published work. The abstract search could also be used to do a lit review, with a “literature pool [that provides] access to publication metadata of more than 35,000,000 documents of many different institutes and universities.” In addition, ResearchGate has a global job search.  There is lots of potential for connecting with relevant researchers in your field, with 200,000 members and growing. Registration required but free.
• Labmeeting – Allows users to organize, collect and share publications and also has a lab management feature. You can create a paper collection, upload EndNote libraries and pdfs, and set alerts to be notified about relevant papers.  The uploading pdfs feature is really nice, because labmeeting can match your pdfs to the correct reference in PubMed, eliminating the need for entering citations manually. In the lab management section, you can schedule events and share protocols in the group notebook. Users also have a profile and the ability to network with colleagues. When I signed up a couple of years ago, a .edu email address was required.  They’ve since restricted membership, so you have to request an invitation, be a member of one of their chosen institutions, or pay a yearly subscription fee ($99).
• MySciNet – Hosted by the AAAS as part of the Science Careers website, “MySciNet is a place for scientists and students from diverse backgrounds to network and build the personal and professional connections needed to succeed in the sciences.” Again, users can set up a profile and join groups (like Women in Science) that fit their interests. What distinguishes MySciNet from the other social networking sites is that it provides practical, relevant advice on how to succeed as a researcher. With articles on how to write a good personal statement, returning to science, and maximizing your mentoring, MySciNet is a valuable resource for navigating the science career path. Registration required but free.
• BioCrowd – BioCrowd is “social network designed exclusively for bioscience professionals.” Described as a cross between Facebook and LinkedIn, which may explain my aversion. It appears to be a pure social networking site/job search site, and may be geared more towards those in industry.  If it’s similar to LinkedIn, I’d be worried about being hounded by headhunters.  They do have a podcast detailing the development of BioCrowd, so I’ll reserve judgment until I give it a listen. Registration required but free.
• CiteULike – Sponsored by Springer, an academic journal publisher, CiteULike is a social reference management website. There’s a basic profile section, groups and connections (your network). You can upload your EndNote libraries and personal pdfs, create watchlists on various topics, and the coolest feature, get recommendations on new articles based on those already in your library. I’ve only been using CiteULike for a few months, but I like it for aggregating articles on my to-be-read list. I have several TOC subscriptions to various journals, and I can click on interesting articles in my email and post them to my CiteULike library for future reading. Registration required but free.
• Mendeley – Similar to CiteULike, Mendeley is a reference manager. It has a web-based interface, along with a desktop client (free download – available for all major platforms, including Linux), making it an EndNote competitor. Mendeley is compatible with both EndNote and CiteULike, so you can easily import your references from these sources.  You can also search journal publishers and other sites directly, and then import interesting articles using the Mendeley bookmarklet. In the desktop client, you can drag and drop your pdfs and Mendeley will automatically extract the citation information. You can read and annotate references in the included pdf viewer. Mendeley also has networking capability, so you can create a research profile, connect with colleagues, and share your annotated articles. There’s also a research trends section, where you can see the articles most viewed by Mendeley users, statistics for publications in your library, as well as your own articles. Registration required but free.
• Connotea – Another online reference manager, geared specifically for scientists and clinicians. The social networking aspects are primitive; the profile page is a text box. References are shared via email links to specific collections in your library. Not crazy about this one, because others are doing it better. Registration required but free.
• Academia.edu – Looks like a Facebook for academics, several members of my graduate department have a presence here. Registration required but free.
• Nature Network – Another Facebook clone, with blogging and discussion forums. Sponsored by Nature. Registration required but free.
• SciLink – I’d actually forgotten that I had an account here, which shows how much I use it.  What I like about it is it generates a network for you based on your publications. Registration required but free.
• ResearcherID – “A Global Community Where Researchers Connect” run by Thompson Reuters, ResearcherID provides scientists with a profile and list of their publications. “With a unique identifier assigned to each author in ResearcherID, you can eliminate author misidentification and view an author’s citation metrics instantly.” It was easier for me to track down all of my citations here, including conference abstracts, and they also provide metrics to measure your impact factor. Registration required but free.
• Epernicus – Another science networking site that I just learned about today, although Richard Dawkins is a member.  Adding publications was fiddly, but there appear to be lots of people from my graduate institution here. Registration required but free.
• ResearchBlogging – You might have noticed the little icon in the last post. As part of my goal to get back to blogging about interesting science, I registered Freethinker’s with ResearchBlogging. Sponsored by SEED, the site aggregates posts on peer-reviewed research which meet their criteria.  It’s a great way to see some of the best work in the science blogging community.

Quite a list, and by no means exhaustive (I left out Laboratree, as I haven’t used it, and it’s primarily a lab management tool). And yet none of these services do everything a researcher would want or find useful. I really don’t think Twitter fills a niche here, except for pointing out interesting articles. I think CiteULike’s recommendation algorithm may be better for that.  Just being a professional Facebook clone isn’t enough, as this wiki details.  The ability to track, import and share publications is critical to collaboration.  Lab management is a nice feature for bench scientists. The threaded conversations and collaboration potential of Google Wave also present network possibilities to researchers.

I’m curious what other scientists think of these online tools.  Do you use them?  Which ones?  Are there particular services you avoid? If so, why?  What would your ideal Science 2.0 experience be?

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Bonetta L (2009). Should you be tweeting? Cell, 139 (3), 452-3 PMID: 19879830

On this Darwin Day, the 200th Anniversary of Charles Darwin’s birth, the 150th anniversary of the publication of his seminal work, On the Origin of Species, and with the election of our new President and his promise to restore science to its rightful place in informing policy, 2009 has been declared the Year of Science by COPUS, the Coalition of the Public Understanding of Science. The Year of Science is intended to be:

a national year-long celebration of science to engage the public in science and improve public understanding about how science works, why it matters, and who scientists are.

NPR did a short interview with one of the organizers of YoS, which you can listen to here.

Last night, the House and Senate agreed on a compromise stimulus package, the American Recovery and Reinvestment Act, which provides more than $15 billion investment in Science and Technology, including:

• $3 billion for the National Science Foundation, for basic research in fundamental science and engineering – which spurs discovery and innovation.
• $1.6 billion for the Department of Energy’s Office of Science, which funds research in such areas as climate science, biofuels, high-energy physics, nuclear physics and fusion energy sciences – areas crucial to our energy future.
• $400 million for the Advanced Research Project Agency-Energy (ARPA-E) to support high-risk, high-payoff research into energy sources and energy efficiency in collaboration with industry.
• $580 million for the National Institute of Standards and Technology, including the Technology Innovation Program and the Manufacturing Extension Partnership.
• $8.5 billion for NIH, including expanding good jobs in biomedical research to study diseases such as Alzheimer’s, Parkinson’s, cancer, and heart disease.
• $1 billion for NASA, including $400 million to put more scientists to work doing climate change research.
• $1.5 billion for NIH to renovate university research facilities and help them compete for biomedical research grants.

More posts on the Year of Science theme will follow.  Today, I am grateful that Congress saw past the limited view of a few Senators (Senators Ben Nelson (D-NE) and Susan Collins (R-ME), in particular), who were working to gut science funding from the stimulus package, and realized that this funding is not only critical to advancing science and technology, but also our economy.

The bill is expected to be on the President’s desk by Monday.

To celebrate the successful first beam test from CERN’s Large Hadron Collider:

Click here to view the embedded video.

“It’s a fantastic moment,” said LHC project leader Lyn Evans, “we can now look forward to a new era of understanding about the origins and evolution of the universe.”

I can’t wait.

I read an article this morning on the New York Times – Literacy Debate: Online, R U Really Reading?

The entire article was interesting, discussing different skills gained by reading online vs. reading books, as well as the concern that online reading may fracture attention spans, making reading books that much more difficult.

What really jumped out at me, though, was this:

Web readers are persistently weak at judging whether information is trustworthy. In one study, Donald J. Leu, who researches literacy and technology at the University of Connecticut, asked 48 students to look at a spoof Web site (http://www.zapatopi.net/treeoctopus/) about a mythical species known as the “Pacific Northwest tree octopus.” Nearly 90 percent of them missed the joke and deemed the site a reliable source (emphasis mine).

Pacific Northwest Tree Octopus

I’m wondering if this lack of critical thinking skills is a side effect of all the information available on the Internet, or if the Internet has just exposed a wider problem, the fundamental lack of critical thinking by a majority of the US population.

This subject has been on my mind recently, due in part to family members who send e-mails “proving” that the presidential candidate they do not support did something horrible, and therefore is obviously not qualified to be leader of the free world, commander-in-chief, etc.  These emails amount to little more than character assassination, and the scary thing is, people believe them and don’t bother to check the facts (easily done online) for themselves.

In the future, traditional reading skills may not be as important as the ability to determine reliable sources, and critical consideration — not just comprehension — of what is read.

I ran across labmeeting.com earlier this week.  The site is a cross between LinkedIn and Endnote:

Labmeeting is a tool for scientists. It was created to help with those things that make doing science needlessly difficult. These include:

• Finding someone at Wisconsin who works on aging in yeast
• Remembering whether the paper about helix bundles was 8753.pdf or science.pdf
• Moving journal club to Tuesday
• Finding out the next time someone gives a seminar on spectroscopy

… and, above all, sharing one’s interests, expertise, and discoveries with others.

With this tool, you can also upload your Endnote libraries (and associated articles), so you have access to your “paper collection” from anywhere. Sharing references with colleagues is a breeze, and there’s even a place to upload lab-specific protocols and post lab events.

Now, I’m off to invite the rest of my lab to join and start uploading papers!

Friedlaender et al. have a recent article in PLos Genetics. Titled The Genetic Structure of Pacific Islanders, the study used 687 microsatellite and 203 indel loci in nearly 1000 individuals from 41 populations in and around Oceania, in order to determine the genetic origins of these populations.

The researchers found

only a modest association between language and genetic affiliation. Oceanic languages were introduced and dispersed around the islands within the last 3,300 years, but there was apparently only a small infusion of accompanying “Austronesian” ancestry that has survived…suggest[ing] that Oceanic languages were adopted by many formerly Papuan-speaking groups, while at the same time there was little genetic influence or marital exchange. At least in Near Oceania, rates of language borrowing and language adoption have been faster and more pervasive than rates of genetic admixture.

Two aspects of this study appeal to me.

1. Whole genome studies appear to be the wave of the future for anthropological genetic research, with the advent of new technologies that make these types of analyses feasible.
2. It was published in an open access journal, by well-respected members of the field. There’s an interesting discussion of open-access publishing at apophenia, in which she emphasizes the importance of tenured faculty supporting open-access.

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Friedlaender JS, Friedlaender FR, Reed FA, Kidd KK, Kidd JR, Chambers GK, Lea RA, Loo JH, Koki G, Hodgson JA, Merriwether DA, & Weber JL (2008). The genetic structure of Pacific Islanders. PLoS genetics, 4 (1) PMID: 18208337

The Public Library of Science (PLoS) has partnered with the National Science Foundation (NSF) and the San Diego Computer Supercomputer Center (SDSC) to create SciVee, which

allows scientists to communicate their work as a multimedia presentation incorporated with the content of their published article. Other scientists can freely view uploaded presentations and engage in virtual discussions with the author and other viewers. SciVee also facilitates the creation of communities around specific articles and keywords. Use this medium to meet peers and future collaborators that share your particular research interests.

It’s still in alpha, so there’s not a lot of content yet. SciVee resembles a cross between LinkedIn and YouTube for scientists, and looks promising. Stay tuned.

An old joke, but serious business for anthropologists and archaeologists studying the introduction of poultry to South America. Introduction of chickens to South America by European explorers had been proposed (or assumed), but Pizarro documented the presence of chickens among the Inca at contact. Researchers at the University of Aukland, using commensal modeling (studying distribution patterns of animals typically found with humans, such as rats, dogs, and domestic species), came to an interesting conclusion published this week in the Proceedings of the National Academy of Sciences.

Examining mitochondrial DNA sequences from 12 samples collected at El-Arenal-1 in Chile, Alice Storey and colleagues found that the sequences match those found at prehistoric sites in Polynesia – Mele Havea in Tonga (2,000-1,550 BP) and Fatu-ma-Futi in American Samoa (AD 700-1390). The chicken bones found at El Arenal-1 were radiocarbon dated to between 1304-1424 AD, meaning they were present on the west coast of South America prior to Spanish or Portuguese contact on the east coast of the continent around AD 1500.

Radiocarbon and DNA evidence for a pre-Columbian introduction of Polynesian chickens to Chile is an important study in two ways. One, it provides the first direct proof of Polynesian contact with South America. (See this post). And since chickens aren’t known for being great fliers, they must have instead come by boat, or in this case, Polynesian sewn plank canoes. Two, it demonstrates what DNA analysis of other types of archaeological remains (not just human) can tell us about human migration patterns.

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Image adapted from Storey, A., Ramirez, J., Quiroz, D., Burley, D., Addison, D., Walter, R., Anderson, A., Hunt, T., Athens, J., Huynen, L., & Matisoo-Smith, E. (2007). Radiocarbon and DNA evidence for a pre-Columbian introduction of Polynesian chickens to Chile Proceedings of the National Academy of Sciences, 104 (25), 10335-10339 DOI: 10.1073/pnas.0703993104

Dr. Richard Leakey, famed paleoanthropologist, has sounded a warning concerning the fate of the world’s great apes, but not from the threat you might expect. While Leakey acknowledges that our closest relatives are at risk due to climate change caused by global warming, he also warned of the risk to biodiversity, including apes, as a result of the human response to global warming, namely the increased reliance on biofuels (think ethanol or biodiesel).

He said that “great swathes” of forest had already been destroyed in South Asia to make way for palm oil plantations [used in personal care products], and this had had a dramatic impact on orangutans, which currently number 50,000.

The pressure to grow cash crops has the potential to accelerate habitat destruction in the world’s poorest countries. Even worse, clear cutting indigenous forests could exacerbate the effects of global warming by decreasing habitats which absorb greenhouse gases.

“It does seem that we cannot stop development, but it does also seem that perhaps we can stop development where critical species are threatened.”

As we attempt to decrease our dependence on fossil fuels and find clean energy alternatives, we must also protect biodiversity on this planet, and ensure that third world countries have sustainable economies, so that they aren’t forced to destroy their natural resources to survive.