17th Sep 2014
Ten Simple Rules for Better Figures
Rougier et al., PLOS Computational Biology 2014
Scientific visualization is classically defined as the process of graphically displaying scientific data. However, this process is far from direct or automatic. There are so many different ways to represent the same data: scatter plots, linear plots, bar plots, and pie charts, to name just a few. Furthermore, the same data, using the same type of plot, may be perceived very differently depending on who is looking at the figure. A more accurate definition for scientific visualization would be a graphical interface between people and data. In this short article, we do not pretend to explain everything about this interface; rather, see [1], [2] for introductory work. Instead we aim to provide a basic set of rules to improve figure design and to explain some of the common pitfalls.
here

Ten Simple Rules for Better Figures

Rougier et al., PLOS Computational Biology 2014

Scientific visualization is classically defined as the process of graphically displaying scientific data. However, this process is far from direct or automatic. There are so many different ways to represent the same data: scatter plots, linear plots, bar plots, and pie charts, to name just a few. Furthermore, the same data, using the same type of plot, may be perceived very differently depending on who is looking at the figure. A more accurate definition for scientific visualization would be a graphical interface between people and data. In this short article, we do not pretend to explain everything about this interface; rather, see [1][2] for introductory work. Instead we aim to provide a basic set of rules to improve figure design and to explain some of the common pitfalls.

here

1st Aug 2014

Jokes That Don’t Work | Context & Variation

Hall created a joke metric he calls the Kardashian Index, which is one’s Twitter followers divided by one’s scientific citations. He writes:

“Hence a high K-index is a warning to the community that researcher X may have built their public profile on shaky foundations, while a very low K-index suggests that a scientist is being undervalued.”

Hall selected a non-random sample of 40 scientists, only 14 of whom were women. He never explains the methods of how he chose these 40. Hall himself says he “had intended to collect more data but it took a long time and I therefore decided 40 would be enough to make a point. Please don’t take this as representative of my normal research rigor.” Why be rigorous and recruit equally when it’s just social science research, amirite?

17th Jul 2014

Committee meeting today! I’ll take this special occasion to share some of my secret presentation tips:

  1. Dolman style shirts. Not only are they stylish, but they make it less obvious that you are sweating profusely.
  2. Be an excellent cook. No one will pay attention to what you are saying when they could instead be eating something delicious. Oreo cookie balls are so easy, you really have no excuse.
  3. Practice talking to yourself in your office/bedroom instead of the coffee shop. Nobody wants to hear you have conversation about genetic diversity with yourself.
  4. The frozen snowball theory.

Good luck!

14th Jul 2014

The 1% of scientific publishing

It would be interesting to see this broken down by subdiscipline.

30th Jun 2014
danidoroi:

The shocking truth about electric fish: Genomic basis for the convergent evolution of electric organs
Writing June 27, 2014 in the journal Science, a team of researchers led by Michael Sussman of the University of Wisconsin-Madison, Harold Zakon of the University of Texas at Austin and Manoj Samanta of the Systemix Institute in Redmond, Washington identifies the regulatory molecules involved in the genetic and developmental pathways that electric fish have used to convert a simple muscle into an organ capable of generating a potent electrical field.
The work establishes the genetic basis for the electric organ, an anatomical feature found only in fish and that evolved independently half a dozen times in environments ranging from the flooded forests of the Amazon to murky marine environments.
"These fish have converted a muscle to an electric organ," explains Sussman, a professor of biochemistry and director of the UW-Madison Biotechnology Center, who first undertook the exploration of the electric organ almost a decade ago. The study published in Science provides evidence to support the idea that the six electric fish lineages, all of which evolved independently, used essentially the same genes and developmental and cellular pathways to make an electric organ, needed for defense, predation, navigation and communication.
"What is amazing is that the electric organ arose independently six times in the course of evolutionary history," says Lindsay Traeger, a UW-Madison graduate student in genetics and a co-lead author of the new report along with Jason Gallant, an assistant professor of zoology at Michigan State University.
Adds Gallant: “The surprising result of our study is that electric fish seem to use the same ‘genetic toolbox’ to build their electric organ,” despite the fact that they evolved independently.
More&Source

danidoroi:

The shocking truth about electric fish: Genomic basis for the convergent evolution of electric organs

Writing June 27, 2014 in the journal Science, a team of researchers led by Michael Sussman of the University of Wisconsin-Madison, Harold Zakon of the University of Texas at Austin and Manoj Samanta of the Systemix Institute in Redmond, Washington identifies the regulatory molecules involved in the genetic and developmental pathways that electric fish have used to convert a simple muscle into an organ capable of generating a potent electrical field.

The work establishes the genetic basis for the electric organ, an anatomical feature found only in fish and that evolved independently half a dozen times in environments ranging from the flooded forests of the Amazon to murky marine environments.

"These fish have converted a muscle to an electric organ," explains Sussman, a professor of biochemistry and director of the UW-Madison Biotechnology Center, who first undertook the exploration of the electric organ almost a decade ago. The study published in Science provides evidence to support the idea that the six electric fish lineages, all of which evolved independently, used essentially the same genes and developmental and cellular pathways to make an electric organ, needed for defense, predation, navigation and communication.

"What is amazing is that the electric organ arose independently six times in the course of evolutionary history," says Lindsay Traeger, a UW-Madison graduate student in genetics and a co-lead author of the new report along with Jason Gallant, an assistant professor of zoology at Michigan State University.

Adds Gallant: “The surprising result of our study is that electric fish seem to use the same ‘genetic toolbox’ to build their electric organ,” despite the fact that they evolved independently.

More&Source

16th Jun 2014
carlsagan:

ah yes, kinesin propagating towards the plus end of a microtubule
i give this fresh cool meme a 10/10

Cellular processes are more boss than we can even imagine.

carlsagan:

ah yes, kinesin propagating towards the plus end of a microtubule

i give this fresh cool meme a 10/10

Cellular processes are more boss than we can even imagine.

(Source: snarkyfancat)

12th Jun 2014
These are not your urban lawn flamingos! This pair dancing in the low tide in Mumbai’s busy harbor are Lesser Flamingos, considered near-threatened species due to declining populations in Africa and India. Yet, over the past decade, some 10-25 thousand of them have been turning up in Mumbai’s Thane Creek to spend the winter right in the middle of a megacity of over 20 million people. I photographed this pair just a year ago at Sewri Port, an industrial dockyard area known more for repairing boats than harboring such wildlife, which now teems in the creek’s recovering mangroves. 
more here
photo: Madhusudan Katti

These are not your urban lawn flamingos! This pair dancing in the low tide in Mumbai’s busy harbor are Lesser Flamingos, considered near-threatened species due to declining populations in Africa and India. Yet, over the past decade, some 10-25 thousand of them have been turning up in Mumbai’s Thane Creek to spend the winter right in the middle of a megacity of over 20 million people. I photographed this pair just a year ago at Sewri Port, an industrial dockyard area known more for repairing boats than harboring such wildlife, which now teems in the creek’s recovering mangroves. 

more here

photo: Madhusudan Katti

10th Jun 2014

Gene editing tool can write HIV out of the picture

If you could do the same thing to prevent massive yield losses in corn, would you?

16th May 2014

jtotheizzoe:

archiemcphee:

Deep Sea Fauna… with Googly Eyes is an awesome site right here on Tumblr that posts photos of amazing deep sea creatures that have been hilariously enhanced with googly eyes. Learn about the myriad mysterious creature of the deep while laughing at their goofy peepers. (Don’t worry, they live way, way far down in the ocean depths. They’ll never know.)

These images are just a small sampling. Head over to deepseafauna for many more.

And what about you? Do you have an urge to googly eye-ify something? Click here to stock up.

It’s Wonderfully Weird Water Friday on Geyser of Awesome!

Scientists have been known to drink a lot.

We take everything and nothing too seriously..

8th May 2014
Synthetic biology: Cultural divide

Although its roots extend back to the early twentieth century, synthetic biology started sprouting as an organized field just over a decade ago. In 2003, only 3 peer-reviewed articles listed in Elsevier’s Scopus database used the term synthetic biology; in 2013, more than 800 did. Last year, the field also marked one of its biggest developments. Capitalizing on a discovery by biochemical engineer Jay Keasling of the University of California, Berkeley, the Paris-based pharmaceutical firm Sanofi began large-scale production of a partially synthetic form of the malaria drug artemisinin, which is normally derived from plants (see Nature 494, 160–161; 2013). And more big advances are in the pipeline: at the Pacific Northwest National Laboratory in Richland, Washington, for example, researchers are creating synthetic fungal enzymes that can convert sugars from broken-down plant biomass into fuels and other industrially useful chemicals.

To patent or not to patent?
more here or here

Synthetic biology: Cultural divide

Although its roots extend back to the early twentieth century, synthetic biology started sprouting as an organized field just over a decade ago. In 2003, only 3 peer-reviewed articles listed in Elsevier’s Scopus database used the term synthetic biology; in 2013, more than 800 did. Last year, the field also marked one of its biggest developments. Capitalizing on a discovery by biochemical engineer Jay Keasling of the University of California, Berkeley, the Paris-based pharmaceutical firm Sanofi began large-scale production of a partially synthetic form of the malaria drug artemisinin, which is normally derived from plants (see Nature 494160161; 2013). And more big advances are in the pipeline: at the Pacific Northwest National Laboratory in Richland, Washington, for example, researchers are creating synthetic fungal enzymes that can convert sugars from broken-down plant biomass into fuels and other industrially useful chemicals.

To patent or not to patent?

more here or here

6th May 2014

Corvids — which include magpies, crows, and ravens — are so clever that some scientists consider their intelligence to be on par with canids, such as wolves, coyotes, and dogs.

3rd May 2014

The butterfly (Dryas iulia) and the bee (Centris sp.) were most likely seeking scarce minerals and an extra boost of protein. On a beautiful December day in 2013, they found the precious nutrients in the tears of a spectacled caiman (Caiman crocodilus), relaxing on the banks of the Río Puerto Viejo in northeastern Costa Rica.
A boat carrying students, photographers, and aquatic ecologist Carlos de la Rosa was passing slowly and quietly by, and caught the moment on film. They watched and photographed in barely suppressed excitement for a quarter of an hour while the caiman basked placidly and the insects fluttered about the corners of its eyes.
De la Rosa reported the encounter in a peer-reviewed letter in the May 2014 issue of Frontiers in Ecology and the Environment.

read more here

The butterfly (Dryas iulia) and the bee (Centris sp.) were most likely seeking scarce minerals and an extra boost of protein. On a beautiful December day in 2013, they found the precious nutrients in the tears of a spectacled caiman (Caiman crocodilus), relaxing on the banks of the Río Puerto Viejo in northeastern Costa Rica.

A boat carrying students, photographers, and aquatic ecologist Carlos de la Rosa was passing slowly and quietly by, and caught the moment on film. They watched and photographed in barely suppressed excitement for a quarter of an hour while the caiman basked placidly and the insects fluttered about the corners of its eyes.

De la Rosa reported the encounter in a peer-reviewed letter in the May 2014 issue of Frontiers in Ecology and the Environment.

read more here

2nd May 2014

montereybayaquarium:

Mystery of the deep! Yesterday we added a deep-sea vampire squid to our Tentacles special exhibition—the first time this species has ever been displayed.

Learn more on our blog

29th Apr 2014

Fire-Setting Ranchers Have Burning Desire To Save Tallgrass Prairie

I work here, no big deal.