Do not FUCK with science bloggers!

My friend and colleague Dr. Danielle Lee had a run in with the man this weekend. Dr. Lee is a postdoctoral researcher in Oklahoma and she writes a blog for the Scientific American Blog Network called The Urban Scientist. She was recently asked by another organization (whom I had never heard of before) called Biology-Online.org to contribute a monthly blog post. After she politely asked if she was going to be paid for her writing she received an unthinkably unprofessional and flagrantly demeaning reply. Aghast that Danielle may want to actually get paid for her work, the representative asked...

"Are you an Urban Scientist or an Urban Whore?"

What. The. Fuck?

Prominent blogger PZ Myers points out the "nuances" of the questioners intonation.

"Urban whore". "Urban" is redneck code for "black". RT @PaulNiland: @jbey why do you claim a race bias also is behind this insult?
— PZ Myers (@pzmyers) October 12, 2013

 In the wake of this electronic slap in the face Danielle took it upon herself to post the e-mail on her blog at Scientific American and record the following video response.  I am absolutely amazed at her composure. I do not think I would have been able to hold back my emotion the way she does here.



So, Scientific American had her back from the start and took steps to sever connection to the person who wrote that e-mail to Danielle, right?

Unfortunately, not exactly.

As we found out later - the legal team at Scientific American got all worked up over Dr. Lee's decision to share the e-mail exchange on a blog with their letterhead on it so they took it down without telling her.

They censored her to cover their asses, that is exceedingly clear.

But to us, their concerned public, SciAm Editor in Chief Mariette DiChristina tweeted this

Re blog inquiry: @sciam is a publication for discovering science. The post was not appropriate for this area & was therefore removed.
— Mariette DiChristina (@mdichristina) October 12, 2013

This was Saturday morning and ZOMG did shit hit the fan. The internet exploded with a veritable rallying cry behind Danielle under the banner #StandwithDNlee. The part about how the post fell outside the mission of "discovering science" epitomizes everything I find frustrating about the old model of media, that there are these shining beacons of truth and that we should really trust brands over people. In this day-and-age words ARE science! Words on the internet are highly traceable data points. There is an entire branch of science emerging that makes hay out of twitter data. Someone will post a graph of #StandwithDNlee trending data over the last three days and I will post it here when I find it. To say that any blog-post on any topic is not about "discovering science" is to be caught unaware about what science on the internet looks like today and will continue to develop into in the future.

After calls to Boycott SciAm from Dr. Isis and fierce push-back from within the very SciAm Blog Network itself Mariette DiChristina issued a more thorough public statement here.

In the statement DiChristina attempts to explain what happened and the precarious timing of it all as this went down on a holiday weekend and so on and so forth.

I wanted more ownership of the fuck-up but hey, people are going to protect their interests first and foremost.

Currently, Dr. Lee's Post is back up and my other hero Bora Zivkovic, the blogfather himself, is doing his best to pull up the mainsail on a network that had a rough weekend. 


If you are sick of all this drama and just want to laugh for a bit. Check out our first #MicroscoParty. I'm posting this so you can witness first-hand the awesomeness that is Dr. Danielle Lee.

@thorsonofodin Sets Sail for Science Online Oceans

@thorsonofodin

Here I am in Miami for the first ever Science Online Oceans Conference.

Despite the fact that this entire genre of science is way outside my wheelhouse I decided to make the trek down from Atlanta. I am curious to see what I learn and who I meet. If it is even a fraction of the intensity of the flag-ship Science Online Conference I attended last February then I am sure I'll be reeling for months.

Leading up to the conference I put together a blog post about the Dead Zone in the Gulf of Mexico. I've been following the political and ecological implications of the dead zone problem for years and decided to summarize the current status of the dilemma.
You can check out that post at Scientific American. A big deal for me as it is my debut piece for the SciAm Network.

Follow the emerging information from this event on Twitter using #ScioOceans.

Some cool links so far...

OMG I want to build one of these DIY mini-submarines! Mom! I can finally build that submarine I dreamed of as a kid! OpenROV 

Want - a navy blue uglifish t-shirt. Awesome - Uglifish

Some sweet web-sites I came across at #ScioOceans.
COSEE Florida
The Echinoblog
Bittel Me This
Ocean Conservancy
Story Collider
Upwell
Deep Sea News 
Society of Environmental Journalism
Plankton Portal


Look at my twitter feed over on the sidebar until I update here ------>

What is this?

Last Friday I held the second MicroscoPARTY. A microscoparty is basically an excuse to nerd-out with friends on the internet with live video from a microscope.

We had a lot of fun but unfortunately the party was not entirely archived as we somehow got cut off about 7 minutes into the discussion. The topic of the evening was food and fungus and we looked at 6 different samples; bread, beer, bread mold, blue cheese, pollen (I know this is not food or fungus but it is EVERYWHERE in Atlanta right now) and finally a drop of fermented tea called Kombucha.

The drop of Kombucha came from a bottle of GT's Guava Goddess.  While perusing the slide I stumbled across the above thing. Full disclosure - I drank a lot of this before sampling so the unknown microbe pictured above may have come from my mouth (though I doubt it). Can you help us identify the curled body in the image? What is this? We have several conjectures from the peanut gallery but I want to conduct an unadulterated survey of TPG readers. Help me crowd-source the answer to this mico-mystery! What is this?

We are All Chemicals - Overcoming Chemophobia

Watch live streaming video from scienceonline at livestream.com

#MicroscopyParty

#SciO13 - Photo Journal

The conference ended late Saturday night. Though I folded myself into crispy hotel sheets my mind would not allow me fall asleep. Every five minutes throughout the night I got up, flipped open my computer and wrote down another idea. It was the first night since high-school I saw the sun rise without sleeping a wink. All thanks to the most epic conference I've ever attended.

Science Online is an annual meeting of people interested in science on the internet. As you can imagine this constitutes a lot of people. To distill the attendees the conference organizers (first photo below) allow a limited number of participants to sign up each year. Sign-up inevitably turns into a race on Twitter. This year I was one of the lucky 450. Like Charlie and his golden ticket I bounded off to Science Online 2013 in Raleigh, North Carolina to take part in a three-day extravaganza of beautiful ideas and new connections.  I met more interesting people in those few days than most people meet in a lifetime. One aspect of the conference I think worth noting was the incredible tolerance that flowed through the entire thing. I was amazed at how rapidly we all connected and immediately formed a large protective family. This was the first time I had been around a large group of people who were all twitter super-users. Indeed part of sign-up required disclosure of our twitter handles. These handles and our names were the only identifiers on our neck-credentials. The speed of connectivity in such an environment is breathtaking. If you have the opportunity to take part in an event like this I highly recommend it.

What follows are pictures and brief descriptions of just a few of those interactions. Over the next few weeks, as my mind mends itself from the internal combustion, I hope to bring you more descriptions and flesh out more ideas born at Science Online.
 

Karyn Traphagen                                                            Bora Zivkovic                                      Anton Zuiker

The organizers of Science Online welcome participants to Raleigh at the North Carolina Natural Science Museum - free to the public and a marvel to behold.

Carl Zimmer - Writes The Loom at National Geographic. Some T.Rex feathers were ruffled among scientists during the #explain session when Carl told the scientists in the room not to unload a textbook on anyone if asked to explain scientific concepts... unless they happen to be writing a textbook. I later unloaded his textbook on him. Carl's comment was taken poorly by scientists as it sounded like he was saying - "you do the science we'll do the journalism." He was later paraphrased by Karen James as saying "Wait, allow me to #journosplain."  I respect Carl and Karen both.  I hope we come to a time in the future when good scientific explanations come about organically from scientists in situ and are not the product of incentives in the publishing biz but then again I am just a naive scientist.

Karen James, who I mentioned above,  is a research scientist and educator. She and I had never met before but bonded while tweeting the Mars Curiosity landing in parallel last fall. I will never forget that night; my enthusiasm for science was set aflame once again. So, I was happy to make her acquaintance in person at Science Online 2013, I even got the chance to have dinner with her and Jonathan Eisen. Listening to them exchange stories about their first trip to the Galapagos Islands and their shared affection for Darwin made me want to buy a plane ticket.

Ed Yong is a renegade science journalist gone legit. He writes a brilliant blog I've followed for years called Not Exactly Rocket Science. NERS recently migrated from Discover Blogs to Nat. Geo.  I wonder how he feels about all the shuffling about that happens as the result of procuring "branded content" as it were. (I always begin writing with a British tone when I think of Edmond)

Kate Clancy is a force to be reckoned with. Thanks to Kate I am now more sensitive to the way I might phrase my explanations of science. #Mansplaining is a pitfall to avoid at all costs. Maintaining self-awareness of how one comes off as a writer and educator is extremely important.  Kate Blogs at Context and Variation. Put her and the rest of this lot up there in your bookmark toolbar!

Mark Henderson is the head of communication at the Wellcome Trust in the UK. He Blogs at the Geek Manifesto. What Can I say, Mark is a hero of mine, up there with Jonathan Eisen and Stephen Curry as crusaders for open access to all knowledge great and small. Bully to the bunch!

Michelle M. Francl was new face for me in world of online science-writing. I am certainly privileged to be connected to her and her brand of writing. She is professor of chemistry on the Clowes Fund for Science and Public Policy at Bryn Mawr College and Blogs at the Culture of Chemistry. Michelle had a phenomenal piece in Slate recently. The piece outlines the perils of irrational fear of "chemicals" it undoubtedly resulted from a session we both attended on #Chemophobia.  I was going to write a piece on this topic and I may still conjure up something of my own but I really do recommend her piece in the interim.

Seth Mnookin is a best-selling author and journalist and is currently co-director of MIT's Graduate Program in Science Writing. He is a contributor to Vanity Fair and blogs with PLoS. I like Seth. We first met in New York City at the 2010 World Science Festival at a panel discussion on Blogs and science-journalism. I sense he is becoming comfortable with his status inside the establishment of science-writing.  Wish time would stop washing revolution from our minds.

I know Jennifer Ouellette because of her presence on the Google+ social network though she is famous in her own right as an author and science blogger. She blogs at Cocktail Party Physics, part of the Scientific American blog network. It is funny how people you've never met before and are not paying any attention to you become like family on the internet. It was through Jennifer's Google+ channel that I first saw the Gangnam Style video.  Ha! She is pictured above inspiring us to use science fiction to explain real science. She encouraged us not to get hung-up on the short-comings of science fiction but to go with it and take liberties to get the audience into a mode of thinking where they can think about big scientific concepts like black-holes or alternate dimensions. I asked her if I could use the tree of Yggdrasil from Norse Mythology as an analogy for the phylogenetic tree of life without running the risk of getting in a creation vs. evolution debate. She gave me the go-ahead with Gusto.  I appreciate her style and hope to stay connected.

And Finally I come to Annalee Newitz. Annalee is editor-in-chief at the best blog in the universe - iO9.  I had only become aware of iO9 over the last year by using a personalized magazine app called Zite. Let me just say, my goodness is iO9 fucking awesome.  I had just read this article on the Evolutionary Biology of Star Trek a few weeks ago and had no idea Annalee wrote it and would be at this conference. How cool is it when you read someone's work before you know you will know them? Really really really cool I say. We got to talk while waiting of for the bus about our favorite TNG episodes. (Mine - Measure of a Man, Annalee's - Darmok, maybe... others were discussed). On top of all this I think the most thought-tastic moment of the whole conference came for me during the #SciFiSci session when Annlee described one utopian/dystopian vision of the future. A vision in which the earth is engulfed by an ever-expanding sphere of technology melded with human consciousness. A physical description of the singularity that sent my frontal lobes swirling into oblivion for several days thereafter. And thus you see why I have had such a hard time writing this first post to summarize my experience at Science Online 2013. It will take me awhile to get it all out there but I hope you stick with me while I try. Thanks for reading and happy Bookmarking!

Uprooting the Tree of Life

Arabidopsis thaliana flower
image - European Research Commission

Hello and welcome to Tom Paine's Ghost. It has been some time since last I wrote a post of any depth. My life has been a whirlwind for the last year and I am only now watching the dust settle. Luckily I still have a big smile on my face. I am currently in Raleigh, North Carolina for my inaugural Science Online conference (if you use twitter look up #SciO13). If the wind doesn't blow me to Kansas I will finally get to meet some big-time science bloggers I've been following for years. The people at this conference are heroes of mine, writers for big international publications, renegades of open-access science journalism, and brothers and sisters-in-arms in the ranks of science. They are people who live and breath science and tell the world about it in compelling new ways. I am delighted to be here and finally to interact with them in the real world!

But before I go live-blogging the Science Online conference I'd like to re-commit to my own blog. To do that I'd better bring you up to date on me my life and where I am now.

At the beginning of 2013 I began a postdoctoral research position in the Biology Department at Emory University. I am continuing to pursue my interest in chromatin structure though I have shifted from test-tubes to whole organisms. As a graduate student at Colorado State I expressed human brain proteins in E. coli and explored how they affect chromatin structure outside living cells in test tubes. Scientists call this kind of work "In Vitro" which is Latin for in glass (glass = test tube). Now I'm working in a plant biology lab that just happens to be interested in chromatin structure as well. The beautiful little plant we work with is commonly known as "mouse-ear cress." Its Latin name is Arabidopsis thaliana.  I can't tell you how much difference it makes to my mood to grind-up plants instead of e. coli for a living.  Now the smell of fresh cut grass wafts from my mortar and pestle while I used to smell that fecal smell you get when you grow up gallons of modified gut bacteria.  It's been a nice transition.  Though I have re-entered science through academia I plan to continue to blog right through. That being said please keep in mind that the opinions expressed here on Tom Paine's Ghost are mine and the authors' I choose to share and do not necessarily represent the opinions of my home institution.

My personal history aside, I have to tell you about a lecture I attended my first week in the Biology Department at Emory.  Charles Kurland, a professor of molecular biology and evolution at the Uppsala University in Sweden came to give a departmental talk hosted by our in-house national academy member - Bruce Levin. During the course of Dr. Kurland's talk I realized he was proposing some radical reshaping of the phylogenetic tree of life.  His overarching claim is that contemporary consensus on structure of the deepest branches is wrong. He claims that his algorithm for sequence comparison does not jive with the accepted models.  This debate may sound esoteric but in this case the conclusions would change biology textbooks across the globe.  It involves the three most ancient roots of the phylogenetic tree of life - The bacteria, the eukaryota, and the archaea.

Common consensus in biology says that the last universal common ancestor (LUCA) of all life was bacteria-like and that this proto-bacteria gave rise to some archaeal ancestor which then gave rise to the first eukaryotic ancestors. Charles Kurland asserts this is not the case.  Professor Kurland uses data from his genomic comparisons to infer the existence of a common ancestor that gave rise to eukaryotes, and then bacteria, and archaea.  At first this seems incredibly counter-intuitive because of course eukaryotes are "more complex" than bacteria and archaea. But Maybe they are just smaller. There is no good reason to think that those organisms have not been evolving in parallel to all other life all along while remaining happily resilient in their tiny forms.

Kurland's hypothesis shakes up the tree of life in several other profound ways.  For one he thinks that all living organisms, the current "crown of phylogeny" as he calls it, is only one bush of biodiversity in a long lineage of expansions  and contractions of life over deep geologic time. He points to the bizarre morphology of the ediacaran fauna as evidence for previous crowns coming to be then dying almost completely due to global climactic events.  Kurland supposes the organism at the base of the current crown of phylogeny to be only a "Most Recent Universal Common Ancestor" (MRUCA) not THE FIRST organism. With this model we would have to accept that it will be impossible to ever theorize about the genetic make up of the first organism on earth because we can never reach past that bottle neck. During his lecture he also pointed out that if random genetic mutation holds steady for all living things over time, then every gene in existence would be fully saturated with mutations within 100 million years. This means that there would be zero sequence similarity between organisms living more than 100 million years from each other.  To me, one of the most fascinating aspects of living things is that when it comes time to reproduce, to replicate the genetic information, it seems that certain genes demand a more rigorous fidelity than others.  Some of the most widely shared genes among all organisms are copied with the most precision and fidelity. Seems like a chicken and egg scenario though.

The other major change to biological consensus Kurland's hypothesis brings to bear is basically a big middle finger to the endo-symbiont theory.  Kurland claims that because the genes for the mitochondrial ribosomes exist and bacteria and mitochondria does not necessarily mean that mitochondria are the remnants of an endosymbiotic bacteria engulfed by primordial life to give rise o the energy-rich cells we all know and love.  Having met Lynn Marguilis before she passed away I know she would take great offense to this suggestion. I wonder who in the community will come to her theory's defense.

Overall the boom/bust cycle of the entirely of life on earth does not seem so far-fetched to me but throwing out the endosymbiant theory seems a bit hasty and at least worth examining further.

All and all a great way to start off my re-entry into science.  Having shaken me to my roots I am forced to accept the fact there there will never be a text book of science ever written that is completely "up-to-date." The minute it goes to press there is bound to be new discoveries overturning old ideas before the ink dries.  Yet another reason to BLOG ON!

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