Field of Science

Showing posts with label blogs. Show all posts
Showing posts with label blogs. Show all posts

People, Content & Technology @ ScienceOnline2010

I am a very frequent attendee and eager participant at scientific conferences: I have logged ~100 in my ~20 years in science. To me, meetings are easily one of the top five things that make being a scientist so much fun. Exchanging ideas (new & old), meeting people (new & old friends), showing off your work (usually new, but sometimes, old), having a good time (which never gets old!)....these reasons are all part of the experience. But sometimes meetings just get you fired up about something(s) and you leave with a fire lit under you. This was one of those for me. And although I knew that I would enjoy myself at Science Online 2010 (aka #scio10) and meet at least some of the criteria above, I was not prepared to leave with my rear side roasting with so many ideas and so much inspiration.

The jazz I got from #scio10 comes from three intertwined categories:

People. Meeting and interacting with people is my favorite conference activity. It's especially great when I first meet someone in person whose work I have followed. This is true for science meetings, but it worked on a wholly different scale for me at #scio10: of the 200+ attendees, I had previously met no more than 10 in person. However, I knew at least 50 more from their online work—mostly science bloggers. Come to think of it, that's probably alot like what happens at a graduate student's first scientific meeting, and I am reveling in that re-found sense of discovering a community that fits. And then there are the people that I met for the first time who I knew nothing about in advance. There are always new people to meet, especially when attending conferences for the first time. But I was stunned by the fraction of people I met who fell in the category of "why did I not know you before?". I can just hope that some of those folks had the same reaction to meeting me!

The intersection of people and content was probably the most amazing thing about this meeting. I have never seen such a meritocracy. Sure, science is based on merit, but there is a real ladder to climb and sometimes a glass ceiling to break. The participants at this meeting ranged from a 9th-grader who writes science computer games to internationally known science journalists (and a HUGE range in between). Many (probably most) of the presenters were self-made experts in newly emerging areas, some in the process of earning PhDs etc., and some that don't need to play in the academic world. Even in the currently-difficult times for both science and journalism (and many other things), there was a clear sense of "Yes we can!" that permeated #scio10 .

Content. The meeting couldn't have started out on a more content-relevant note for me: the first session I attended was "From Blog to Book: Using Blogs and Social Networks to Develop Your Professional Writing"As I am now digging into my sabbatical book project, this session jolted me to attention. The advice of Tom Levenson, Brian Switek and Rebecca Skloot was just what I needed. I must decide very soon whether to pursue the academic publisher route or to try the trade route taken by authors of most successful popular science books. Next on my schedule was "Rebooting Science Journalism in the Age of the Web" in which a panel discussed the sometimes uneasy ecosystem of blogs and more traditional media outlets. The somewhat controversial press-release site, Futurity, created some heat (and maybe some light), but the memorable lesson by Carl Zimmer about his reporting on the twisted biology of duck penises generated the most virulent meme of the whole meeting. In the third morning slot I joined the "Scientific Visualization" session in which Tara Richardson (@science_goddess) regaled us with the latest cool tools and facilitated some interesting discussion on this under-appreciated (and thus, under-developed) aspect of science communication.

On Saturday afternoon, I attended the helpful session "Scientists! What can your librarian do for you?"which reminded me that I can almost certainly make use of those smart people whose mission is to help me do my science (and writing) better. Next was "Open Access Publishing and Freeing the Scientific Literature (or Why Freedom is about more than just not paying for things)" moderated by friend and colleague Jonathan Eisen (aka @phylogenomics; pictured above). It's going to be a tough road to OA publishing, but I am starting to see that it is a fight worth waging. For the final session of the day, I joined the packed-to-the-gills session "Writing for more than glory: Proposals and Pitches that Pay" moderated by Rebecca Skloot with key insight from Ivan Oransky and Clifton Wiens. Although much of the session was aimed at pitching stories to magazines, there was a fair bit of discussion of book proposals and how to craft a project that publishers will buy—literally. Much to my chagrin, the first lesson was that the pitch "My book is on X" doesn't fly. Stories sell books and topics don't. OK, more homework for me...it might be a good thing that my book is "on Sex", but that isn't enough. So when the participants were invited to give their pitch to the experts, I knew that I wasn't up to snuff. However, shark researcher (and future author) David Shiffman (@whysharksmatter) bravely jumped right in—to our benefit. The most memorable line from the pitch-dissection was 'NPR is more important than PhD'; since David had been interviewed on NPR. Indeed, as I later found out to my surprise, David doesn't have his PhD (yet).

After a great banquet and party on Saturday night, I was ready to go again on Sunday morning, starting with "Broader Impact Done Right" hosted by a panel of postdocs, grad students and science communicators. The opening film, in which various portrayals of scientists in movies and television made us both laugh and cringe, presaged some great discussion about how we can appeal to various constituencies that we really need to reach. Since I wanted to hear more about science journalism, I next attended "Getting the Science Right: The importance of fact checking mainstream science publications — an under appreciated and essential art — and the role scientists can and should (but often don’t) play in it" I was surprised to learn about how unevenly the fact-checking is done, and when it is done, how arduous and expensive it can be! In the category of saving-the-best-for-last, the final session that I attended was "Blogging the Future – The Use of Online Media in the Next Generation of Scientists" in which a group of high school students from Stacy Baker's Biology Class individually presented their projects, ranging from an analysis of student use of blogging and the social web for education and fun to iPhone application development for science learning. These kids absolutely stole the show with their poise and content, giving many of us renewed confidence for science and its communication in the future.

Technology. As if the people and content weren't enough, in these three short days I also experienced some serious surges in my use of and appreciation for technology. For the first time ever, I didn't bring a pen or pad of paper to the meeting. I took all of my notes on my iPhone, which was the only device I used while onsite. In my office is a two-foot pile of legal pads and notebooks containing mostly illegible notes from 20 years of previous meetings. But in my difficult transition from paper to electrons (I am a very slow keyboard typist), I have gotten lazy about note-taking over the past years. So I was glad to find out for myself that I am a reasonably adept two-thumb note taker! And I can email myself my notes with one click!

I also jumped in with both feet to Twitter. As an occasional tweeter (@johnlogsdon), I use the medium for some things, but I had not yet figured out the ratio of function:fun. By using the hashtag #scio10 all of the meeting tweets were instantly readable by all of the twitter-ers (onsite & off) in REAL TIME. By the end of Day 1, I was hooked. As of writing, my total (13-month) tweet count is 235—of which ~70 were sent during the three days #scio10 (which currently total >6300)! Granted, some of those tweets were part of the fun game played at Saturday's banquet, in which the fastest tweet with the right answer won a prize. I apparently have mastered speed-tweeting, since I won one of the prizes: a signed copy of Rebecca Skloot's forthcoming book "The Immortal Life of Henrietta Lacks" (see image above).

There's so much more that I didn't say here, but I hope that my account will give you a sense of how pleased I am to have participated in #sci010. Thanks to Bora Zivkovic (pictured above), Anton Zuiker and everyone else (including the generous sponsors) who contributed to ScienceOnline 2010!

Mary Roach orates on orgasms

Mary Roach is the author of Stiff, Spook, and most recently—and very relevant to me—Bonk . She gave a very entertaining TED talk on "Ten things you didn't know about orgasm". It's both funny and informative.

I read Bonk last summer (?) and while I enjoyed much of it, I also had some mixed feelings. Perhaps I'll put together a review sometime.

In the meantime, enjoy...


Thanks to Pleiotropy for the lead.

SG&E has joined Field of Science (FoS)

Just when I thought that I would leisurely make my way back into blogging...

Over the weekend I got an invitation from Edward, the editor and proprietor of Field of Science, to join his stable of blogs. I was already a follower of Steven Salzberg's blog Genomics, Evolution and Pseudoscience which had recently moved to FoS. So I shot Steven an email to seek his advice, and on his hearty recommendation, I joined with little hesitation.

Now after little more than a day, I'm here with a brand spankin' new look and feel to my blog. I hope that you will enjoy it. Thanks, Edward!

On sabbatical at NESCent!

After many months of blogging hiatus, I am planning to get back in the groove over the next few months. Starting this week, I am a sabbatical scholar at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina. I'll be here through July, 2010. My major project will be to write a semi-popular book on the origin and evolution of sex. This will also be a great opportunity for me to recharge my batteries and to tie up some loose ends that have been accumulating.

I plan to use this blog venue to sketch some ideas that might end up in my book, so I hope that I'll be able to re-gain (or perhaps newly gain) your attention and comments! Stay tuned...

P.S. I'm twittering @johnlogsdon

Dodos: Free in Iowa City!

Tomorrow (Monday, Sept. 22) in Iowa City I will be co-hosting a free public screening of "A Flock of Dodos" in Biology Building East (BBE) 101 at 7:00pm. This event is part of Scienceblogs 10^6 comment festival, via our two Iowa City-based ScienceBlog-ers, Tara Smith (Aetiology) and Evil Monkey (Neurotopia). It is also associated with the Evolution undergraduate course (Biology, 002:131) that I teach with Bryant McAllister (can you say "extra credit"?)

According to Wikipedia:
"The film attempts to determine who the real "dodos" are in a constantly evolving world: the scientists who are failing to promote evolution as a scientifically accepted fact, the intelligent design advocates, or the American public who get fooled by the "salesmanship" of evolution critics. While Randy Olson ultimately sides with the scientists who accept evolution, he gives equal air time to both sides of the argument..."
Thanks to the filmaker Randy Olson for allowing us to screen this film for the public! I'm looking forward to it, since I have not seen it yet.

Publishing by Press Release: PNAS Lags Again

Here we go again...

I got an email message on Tuesday (August 26th) from the NSF announcing the publication of an apparently interesting and provocative new paper by Song et al. The message linked to a press-release from NSF (dated August 25th) entitled "DNA Barcodes: Are They Always Accurate?"

According to the NSF Press Release:
"DNA barcoding is a movement to catalog all life on earth by a simple standardized genetic tag, similar to stores labeling products with unique barcodes. The effort promises foolproof food inspection, improved border security and better defenses against disease-causing insects, among many other applications.

But the approach as currently practiced churns out some results as inaccurately as a supermarket checker scanning an apple and ringing it up as an orange, according to a new Brigham Young University (BYU) study.

The results are published online this week in the journal Proceedings of the National Academy of Sciences (PNAS)."
After repeatedly checking the PNAS Early Edition website all last week, I see that paper in question was finally released on Friday (August 29). It's even fully Open Access!

Hojun Song
, Jennifer E. Buhay, Michael F. Whiting and Keith A. Crandall "Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified" PNAS published August 29, 2008, doi:10.1073/pnas.0803076105

Dark Matter

A follow-up on a blog post from last year...

According to The First Post:

"The release of a new Meryl Streep movie about a campus killing spree, which was postponed last year after the shooting of 32 people at Virginia Tech, will not be delayed again – despite the recent spate of campus killings, including the gunning down of five students in a classroom at Northern Illinois University on St Valentine’s Day. Dark Matter is based on the true story of Gang Lu, a Chinese graduate student at the University of Iowa who shot and killed five people and paralysed another before killing himself in 1991. In real life, Lu's rage was fueled by his belief that he should have received honours for his doctoral dissertation that were instead awarded to a fellow student."
Here is a link to movie's website. (There is now a trailer that you can watch: Updated 7/29/08)

Science Debate

"Given the many urgent scientific and technological challenges facing America and the rest of the world, the increasing need for accurate scientific information in political decision making, and the vital role scientific innovation plays in spurring economic growth and competitiveness, we, the undersigned, call for a public debate in which the U.S. presidential candidates share their views on the issues of The Environment, Medicine and Health, and Science and Technology Policy."
Chris Mooney and Sheril Kirshenbaum over at The Intersection have assembled a crack list of scientists and science bloggers to launch the the ScienceDebate2008 website. If you are so inclined, go over and pledge your support. They have also set up rapidly-growing groups over at facebook and myspace.

I'm an Intellectual Blogger

The Evilutionary Biologist (aka John Dennehy) has tagged me with an Intellectual Blogger Award. Given my serious lack of posting lately, I'm not sure that I deserve it...but thanks!

The award traces to An Unquiet Mind where the stated rules are:
This award is intended for those bloggers who demonstrate an inclination to think on their own. This is what I think is needed in today’s blogosphere. The term ‘Intellectual’ has often been derided in recent times, and this is one way to resurrect the true meaning: “An intellectual is one who tries to use his or her intellect to work, study, reflect, speculate on, or ask and answer questions with regard to a variety of different ideas.” The rules are:

1. If, and only if, you get tagged, write a post with nominations for 5 blogs that you think are of “Intellectual Bloggers”.
2. Optional: Link to this page so that people can easily find the exact origin of the meme.
3. Optional: Proudly display the ‘Intellectual Blogger Award’ with a link to the post that you wrote.
I hereby nominate:
  1. Tree of Life (Jonathan Eisen; even though he doesn't like these memes)
  2. Aetiology (Tara Smith)
  3. Twisted Bacteria (Cesar Sanchez)
  4. Small Things Considered (Elio)
  5. Evolgen (RPM)
and one that I was suprised to find has apparently not yet been included:

Promoting Plants at the Expense of Fungi?

Ryan Gregory, over at Genomicron, found an interesting tidbit on the Discovery Channel website entitled Plants and Animals: Long-Lost Relatives?. He is surprised to read that
"organisms such as fungi should be given a demotion — placed further from animals on the tree — while green plants should get a leg up."
This is the case, apparently according to a recently-published paper from John Stiller at East Carolina University.

Gregory is (rightfully) annoyed at the suggestion of any group "getting "demoted" one way or another because this idea of rank (was) should have been abandoned 150 years ago." and that was the main point of his post. Ryan has been (again, rightfully) critical of science reporting and this doozey has all of the right parts, as detailed in his Anatomy of a bad science story.

However, there have been a series of comments about the veracity of the Stiller paper, so I thought I would make a few of my own here. First of all, it should be duly noted that the paper in question, Plastid endosymbiosis, genome evolution and the origin of green plants, is explicitly labelled as "Opinion"; this is on top of the fact that it is published in the review journal TRENDS in Plant Science—not a primary research venue. Neither of these facts are damning to the work, but they certainly suggest caution in reporting the findings.

Second, it is fair to say that this hypothesis (wrongly called "Stiller's theory" by the Discovery story) is way out of the mainstream of current thought. Again, this alone should neither preclude the publication nor, by itself, lend it to immediate scorn. It's great to see such examples of how science works in the marketplace of ideas. But we all know that just because something gets published, does not mean it's right.

In any case, there are two main components that Stiller argues in this paper:
  1. that the "Plantae" [Viridiplantae (green algae & land plants), Rhodphyta (red algae) and Glaucocystophyta] are not a monophyletic group, and
  2. that the Viridiplantae are more closely related to animals than are fungi.
The data on "Plantae" monophyly are certainly not so compelling as to rule out other possible answers. But recent work (here and here) is increasingly providing support for this relationship. Stiller has been a long-standing contributor to the literature on non-monophyly of green+red algae. I have worked on some of the same molecules that he has (i.e., RNA pol II) and he might have a point for there not being strong support in favor of "Plantae". However, I don't think that there is an alternative that garners anywhere near the consistent support that "Plantae" gets in multigene trees.

The data on the sisterhood of animals and fungi grouping to the exclusion of plants (e.g., Viridiplantae) is about as solid as deep relationships among eukaryotes can be. A nice summary of these results was recently presented in PLoS Genetics. Since the paper is Open Access, I won't repeat the findings here (full disclosure: although I am not an author of this paper, I do collaborate with them). Suffice it to say that there is not even a hint of evidence that Viridiplantae is closer to animals that are fungi as suggested by Stiller. Note also that these authors are not particularly bullish on "Plantae" either.

Stiller cites the presence of certain enzymes and protein domains in both plants and animals (apparently absent in the fungi) as evidence for a closer relationship of plants to animals. But the problem is that such things only have to be lost once in the fungal lineage (if they have been lost at all) to make these cases complete non-sequiturs. To explain why plants don't fit in with animals, Stiller would rather invoke some sort of bias in the data. Although such biases may exist, I am very cautious about invoking an entire reworking of the tree based on them.

Stiller ends with four "Future Perspectives" of which I find the following most telling:
"There should be no a priori assumption that the strongest tree-building signal in a given data set reflects evolutionary history rather than bias in the data."
I'll file that in the category of "Things that make you say Hmmm".

Favorite Science Blogs

As ususal, I am late to the party where everyone is discussing their favorite science blogs. This was a no-RSVP-required affair that The Scientist has been hosting under the banner of "Vote for your favorite life science blogs". Most of my favorites are listed in the "Other Interesting Blogs" on the left of my blog. I actually use this list as my major navigation tool for blog-visiting. Of these, here are my most frequently-visited (and therefore most favorite):

Daily (or throughout the day):

Sandwalk. Bravo, Larry!
Pharyngula. Does PZ sleep?
Tree of Life. Jonathan says things that I wish I would have said (& some I'm glad I didn't).
FemaleScienceProfessor. Wow. FSP is anonymous and it really works!

Slightly less than daily:

Aetiology
Evolgen
Fungal Genomes & Comparative Genomics
Genomicron
Scientia Natura
The Evilutionary Biologist
The Loom

More than weekly:
all the rest.

Joe Biden on Science Funding

Iowa is a great place to be if you are at all interested in national politics. Case in point: last Thursday I found myself in the same place as presidential hopeful Joe Biden. He was at the University Bookstore signing copies of his book, "Promises to Keep: On Life and Politics". The line wasn't very long, and I consider Joe to be one of my top three candidates this year. So I ponied up the $27 to buy a copy so that I could get him to sign it and throw a few questions at him.

I introduced myself as a Biology Professor and asked him about his thoughts on basic science funding. Without hesitation, he said that he would support a doubling of the NIH and NSF budgets. When I asked if I could post that comment on my blog, Biden agreed. He also was keenly aware that the although funding for both has increased in recent years under the current administration, it has not been effective at increasing basic science. I don't know how much of that was just telling me what I wanted to hear, but I was pleased.

He signed my book "Keep the faith. Keep on teaching" I don't know about the former....

On a related topic, check out the following link that matches your views to those of the current presidential candidates.

Dawkins Defends the OUT Campaign

Although I am a bit late to the party, I wanted to point OUT that Richard Dawkins has recently posted a nice essay about the OUT Campaign and why it is necessary. Here is a snippet:
"Our choir is large, but much of it remains in the closet. Our repertoire may include the best tunes, but too many of us are mouthing the words sotto voce with head bowed and eyes lowered. It follows that a major part of our consciousness-raising effort should be aimed, not at converting the religious but at encouraging the non-religious to admit it – to themselves, to their families, and to the world. This is the purpose of the OUT campaign."
PZ has already added his few cents to this and as I post, there are are already 319 comments.

Picture credit here. Thanks Matti A.

The OUT Campaign

image

Sorry for the long haitus & thanks for staying tuned! Summer time has been keeping me busy this year.

So, what does this big red "A" above mean? Click it and find out for yourself. The folks over at RichardDawkins.net have launched an internet effort to let the world know that there are alot of us OUT there. I'm happy to be OUT. Here's a snippet from the site:
"As more and more people join the OUT Campaign, fewer and fewer people will feel intimidated by religion. We can help others understand that atheists come in all shapes, sizes, colours and personalities. We are labourers and professionals. We are mothers, fathers, sons, daughters, sisters, brothers and grandparents. We are human (we are primates) and we are good friends and good citizens. We are good people who have no need to cling to the supernatural."
When you see the A, you know!

Blogging for good

T. Ryan Gregory over at Genomicron asks: How much good can one blog post do? In a very moving post about the efforts of his father and stepmother to make a difference in Livingstone, Zambia, he asks us to help them in whatever way we can (suggestions are given).


The Livingstone Performing Arts Foundation (LiPAF) mission is to create and perform traditional and original works of music, song and dance which reflect the history, culture, languages and ethnic background of Zambia. Operating as a not for profit organization, LiPAF will enrich the community by providing opportunities for employment, sponsorship of a variety of needy programs and services, and educational programs on topics related to the human condition.





Tagged?!?

I have been tagged by Shalini over Scientia Natura, Here are the rules:
(although I don't think that she followed #5)
  1. We have to post these rules before we give you the facts.
  2. Players start with eight random facts/habits about themselves.
  3. People who are tagged need to write their own blog about their eight things and post these rules.
  4. At the end of your blog, you need to choose eight people to get tagged and list their names.
  5. Don't forget to leave them a comment telling them they're tagged, and to read your blog.
1. I consider myself a native Iowan. Although I was born in Missouri (1965), I grew up in Iowa (1968-1983) and went to Iowa State University as an undergraduate (1983-1988). After various academic stints elsewhere, I returned in 2003 to join the faculty at the University of Iowa.

2. I shook hands with Dave Loebsack today at the Coralville 4th of July Parade. Dave is our freshman Democrat congressman who beat out long-standing incumbent Republican Jim Leach last fall. I asked Dave to "keep up the good work" and to pay particular attention to health care and science funding. He assured me that he will do so.

3. I have a motorcycle, but I don't ride it enough. It's a 1995 Honda Shadow VT600C that I got when I finished my PhD 12 years ago. I have been planning to upgrade to a bigger bike someday (a Harley Fat Boy would be nice).

4. I spent a year studying abroad at University College, Swansea (now Swansea University) in Wales as an undergraduate (1985-1986). I took philosophy and psychology courses there because I was unsure about biology at that time.

5. I like my coffee black and my art abstract. Peets Arabian Mocha-Java is my favorite coffee. Rothko and Pollack are among my favorite artists.

6. I played baritone sax when I was in high school. I was particularly interested in jazz and even once won a solo contest at the state level. I considered a music major in college, but quickly realized that I was not as prepared (and committed!) as I needed to be. Lately, I have been considering picking it back up (but I need to buy one first!).

7. My entire academic lineage is comprised of Members of the National Academy of Sciences. My undergraduate mentor, Steve Briggs, is now at UC San Diego. My PhD advisor, Jeff Palmer, is at Indiana University. My post-doc advisor, Ford Doolittle, is at Dalhousie University. I am proud of the accomplishments of my mentors, but they have placed the bar rather high!

8. I eat chocolate at least once a day. Almost anything will do. Snickers and Skor bars are standard fare, but I also enjoy high-end treats.

I hereby tag:

Commenting to each of these blogs (aka Rule #5) will now commence!

Another Fun Blogger Gathering

I returned home late on Sunday (Canada Day!) from Halifax, Nova Scotia where I was attending the Society for Molecular Biology & Evolution (SMBE) annual meeting and the immediately following Canadian Institute for Advanced Research (CIfAR) Program in Evolutionary Biology meeting. There was lots of good science and one highlight was a dinner get-together of a few bloggers and blog-readers. Bloggers included in our group were RPM, Rosie Redfield, Jason Stajich, Reed Cartwright, and Jacob Tennessen. Both Reed and RPM have posted more about this gathering, including a complete list of attendees (pictured left). Thanks everyone for an enjoyable time! This is an activity that I hope to continue...

Why Rosie doesn't work on Sex

My friend and colleague, Rosie Redfield, has written an interesting post about the origin of eukaryotic sex, entitled "Why I don't work on sex in eukaryotes ". She sums up what we do and don't know about deep eukaryotic relationships and how this impinges on the origin of sex and meiosis. One bottom line is that we still don't know what the earliest branch on the eukaryotic tree is. The other is that it might not matter for the origin of meiosis since work in my lab has shown that homologs of meiotic genes are present in all of the major protist lineages (e.g, this paper, but stay tuned for more details...). Rosie ends her provocative post by paying me a sincere compliment:
"I'm glad that John Logsdon has been working on this, rather than me."
Thanks, Rosie!

Microbial-bloggers

As I mentioned a few weeks ago, a few science bloggers got together in Toronto while some of us were attending the American Society for Microbiology general meeting. ASM's MicrobeWorld (a.k.a Chris Condayan) captured us on video. My colleague Tara Smith reported on this earlier today, as did Ryan Gregory. Addendum: Jonathan Badger also reported on this.

WARNING! (or, now I'm really proud?)



This rating was determined based on the presence of the following words:
* sex (20x) * penis (4x) * sexy (3x) * drugs (1x)

All of this "improvement" in just one day?!