Tag Archives: University of Washington

Little skates, mermaid purses, nature, and writers

GrrlScientist has written a fascinating ;piece about skates (fish), poetry, and Twitter for her Dec. 5, 2013 posting on the Guardian Science Blog network (Note: A link has been removed),

Twitter is a wonderful medium. For example, a couple days ago, I met University of Washington Biology Professor Adam Summers on twitter. It turns out that he is Associate Director of Friday Harbor Labs, where I spent a summer taking an intensive molecular neurobiology course during my graduate training in zoology. …

“Skates are fabulous animals”, Professor Summers writes in email.

“They make up a quarter of the diversity of cartilaginous fishes and every darn one of the 250 species looks pretty much exactly like every other one.”

Thus, studies into the anatomy and development of one species may provide insight into these processes for other, rarer, species.

“The little skate, also called the hedgehog skate, was one of my go-to organisms for many years”, writes Professor Summers in email.

These studies provide the basis for a physical or a mathematical model that may help understand function. This model is of course tested both against its inspiration and as a predictive tool. For example, the skate’s tail is very important, even for the developing embryo.

“I figured out that it can’t survive on the oxygen that diffuses through the capsule. Instead it has to pump water through by vibrating its tail.”

Perhaps this is the reason that the tail muscles differ from what’s considered normal.

“A wonderful muscle physiologist showed that the muscle in the tail is cardiac muscle rather than the striated muscle it should be”, Professor Summers writes.

While colleagues thought Summers’ specimens were good enough to be compared to visual art, his little skate specimens also inspired a poet (from the posting),

“I got chatting with a friend who teaches a poetry class up here [at Friday Harbor]. Sierra Nelson and I had several long conversations about the similarity of the lens that poets and scientists bring to the world.”

“I think the poem does a much better job of engaging the viewer than my dry prose on the critter.”

Little Skate
Leucoraja erinacea

Littlest of little skates, just barely hatched!
You can still see the remnants
of my yellow egg sac.

And my tail’s a little longer
than my whole body
(I’ll grow into it more eventually).

….

Adam Summers shared one of his images of his ‘stained’ little skate specimens on his twitter feed (pic.twitter.com/UWCKeVMmYB)

Here's an embryo of the little skate, Leucoraja erinacea. pic.twitter.com/UWCKeVMmYB

Here’s an embryo of the little skate, Leucoraja erinacea. pic.twitter.com/UWCKeVMmYB

I recommend reading GrrlScientist’s posting (Inside a mermaid’s purse; A poetic intersection between life and science, art and photography) for the whole story and, for that matter, the whole poem. As for the mermaid purse, this is the name for the little skate’s egg sack when found on the beach.

This all reminded me of Aileen Penner, a writer, poet, and science communications specialist located in Vancouver, Canada and her work in science and creative writing. She wrote a Nov. 19, 2013 posting about the intersection of nature and writing titled: US Forest Service Scientist Says Writers Help Gather “Cultural Data” on our Relationship With the Natural World (Note: Links have been removed),

Who is Fred Swanson you ask? Yes he is a retired U.S. Forest Service scientist and yes he is a Forest Ecology Professor at Oregon State University (OSU), but he is also a key figure in the Spring Creek Project for Ideas, Nature, and the Written Word. This is a program I have been following since 2006 and greatly admire for their commitment to bring together “the practical wisdom of the environmental sciences, the clarity of philosophical analysis, and the creative, expressive power of the written word, to find new ways to understand and re-imagine our relation to the natural world.”

In April of 2012, I went to OSU to interview the Director of the Spring Creek Project, Charles Goodrich. I wanted to know how to fund such a long-term interdisciplinary project. Charles talked a lot about Fred Swanson and his enthusiasm for having writers as part of the inquiry process and about Swanson’s personal commitment to writing the arts into scientific funding proposals for his work at the H.J. Andrew Experimental Forest.

Penner was inspired by an Andrew C. Gottleib article (About Earth Scientist Fred Swanson) in Terrain’s Fall 2013 issue and quotes from it throughout her own posting. She also notes this (Note: Links have been removed),

Terrain interviewer Andrew Gottlieb will moderate a panel “Artists in the Old-Growth” with Alison Hawthorne Deming, Fred Swanson, Charles Goodrich and Spring Creek Project Founder, Kathleen Dean Moore at the upcoming AWP conference in Seattle on February 27, 2014. If you are in Seattle for this – go see it!

Before investigating the Association of Writers and Writing Programs (AWP) 2014 conference and the special session any further, here’s a bit more information about the Spring Creek Project for Ideas, Nature, and the Written Word, from the homepage,

Spring Creek Project engages the most daunting and urgent environmental issues of our times while remembering and sharing our perennial sources of joy, wonder, and gratitude. We are a convening organization that sponsors writers’ residencies, readings, lectures, conversations, and symposia on issues and themes of critical importance to the health of humans and nature. We believe sharing insights, inspiration, and methods from many perspectives increases our understanding of the place of humans in nature. Our goal is to include participants and audience members from every discipline and persuasion, from creative writing and the other arts, from the environmental and social sciences, from philosophy and other humanistic disciplines.

The AWP conference seems mainly focused on fiction and literary nonfiction (at least, that’s what the video highlights [on the 2014 conference homepage] of the 2013 conference would suggest). Here’s more from the 2014 AWP conference homepage,

Each year, AWP holds its Annual Conference & Bookfair in a different city to celebrate the authors, teachers, students, writing programs, literary centers, and publishers of that region. More than 12,000 writers and readers attended our 2013 conference, and over 650 exhibitors were represented at our bookfair. AWP’s is now the largest literary conference in North America. We hope you’ll join us in 2014.
2014 AWP Conference & Bookfair

Washington State Convention Center &
Sheraton Seattle Hotel
February 26 – March 1, 2014
Key Dates:

November 8, 2013: deadline for purchasing a conference program ad
November 15, 2013: offsite event schedule opens
January 22, 2014: preregistration rates end
January 23, 2014: will-call registration begins
February 26, 2014: onsite registration begins

Here are some details about the R231 Artists in the Old-Growth: OSU’s Spring Creek Project & the HJ Andrews Experimental Forest
AWP 2014 conference session,

Room 602/603, Washington State Convention Center, Level 6
Thursday, February 27, 2014
3:00 pm to 4:15 pm
How can a residency program empower and generate inquiry and creative responses to our astonishing world? How can a long-term, place-based program affect the way we see our relation to the forest? The world? Join this discussion with the founders and participants of the Oregon State University-based Spring Creek Project that brings writers to a place of old-growth forest and ground-breaking forest science.

Andrew Gottlieb Moderator

Andrew C. Gottlieb is the Book Reviews Editor for Terrain.org, and his writing has appeared in journals like Ecotone, ISLE, Poets & Writers, and Salon.com. He’s the author of a chapbook of poems, Halflives, and he won the 2010 American Fiction Prize.
Fred Swanson

Fred Swanson co-directs the Long-Term Ecological Reflections program based at the H.J. Andrews Experimental Forest in the Oregon Cascade Range, which has hosted more than forty writers in residence and a variety of humanities-science interactions. He is a retired US Forest Service scientist.
Kathleen Dean Moore

Kathleen Dean Moore is an essayist and environmental ethicist, author of Riverwalking, Holdfast, Pine Island Paradox, and Wild Comfort, and co-editor of the climate ethics book, Moral Ground. She is co-founder and now Senior Fellow of the Spring Creek Project at Oregon State University.
Alison Deming

Alison Hawthorne Deming is author of four poetry books, most recently Rope, and three nonfiction books with Zoologies: On Animals and the Human Spirit forthcoming. She is Director and Professor of Creative Writing at the University of Arizona.
Charles Goodrich

Charles Goodrich is the author of three books of poetry, A Scripture of Crows; Going to Seed: Dispatches from the Garden; and Insects of South Corvallis; and a collection of essays, The Practice of Home. He serves as Director for the Spring Creek Project for Ideas, Nature, and the Written Word

One last note about nature and writing, I interviewed Sue Thomas, author of Technobiophilia: nature and cyberspace, in a Sept. 20,,2013 posting about her book and other projects.

Your grandma got STEM?

Jeff Bittel thank you for a story (Mar. 26, 2013 on Slate) about Rachel Levy and the website where she gently blows up the notion/stereotype that older women don’t understand science and technology and that they are too old to learn (Note: A link has been removed),

 Is your grandmother a particle physicist? Did she help the Navy build submarines or make concoctions of chlorine gas on the family’s front porch? Or is she a mathematician, inventor, or engineer? If so, then baby, your grandma’s got STEM.

Grandma Got STEM is a celebration of women working in and contributing to the fields of science, technology, engineering, and mathematics. It is also designed to combat the doting, fumbling, pie-making stereotype of grandmatrons.

That’s why Rachel Levy, an associate professor of mathematics at Harvey Mudd College, is collecting the stories of grandmas across the various fields of STEM. She first got the idea after hearing someone utter the phrase, “Just explain it like you would to your grandma.”

At first blush, such a thing seems harmless. But think about what it means—basically, all older women are stupid.

“For two or three years I thought about how I could address this issue without just making people angry and more inclined to use the phrase,” Levy told me. “If I could come up with a million examples of grandmothers who were tech-savvy, people wouldn’t say it anymore because it wouldn’t be apt.”

While attending the conference ScienceOnline this year, Levy realized she could harness the power of the Internet to collect stories and showcase them. So far, she’s been able to upload at least one grandma a day for about a month and a half—and the stories keep pouring in. Levy’s aim so far is to be as inclusive as possible. She’s accepting any grandma currently or previously involved in STEM. They can submit themselves or you can submit for them. Heck, they don’t even have to have children with children, per se. Age’ll do just fine.

Bittel might want to reconsider that bit about children and children with children. That can be a touchy topic.

Levy’s solution was to create the Grandma Got STEM website. From the Mar. 27, 2013 posting about Mary Vellos Klonowski,

GrandmaGotSTEM

Thank you to undergraduate Math/Computer Science Major Joey Klonowski, who submitted this post about his grandmother:

This photo is from the October 3, 1951 edition of The Southtown Economist, a daily newspaper on the South Side of Chicago, when my grandmother, Mary Klonowski, was 18. She attended DePaul University against the wishes of her father, who didn’t want his daughters to be college educated. She received a BS from DePaul in 1954 and was the only woman chemistry major in her class. She later earned a master’s in mathematics education and became a high school math teacher. She is now 80 years old and still working as a substitute teacher.

There are a lot of stories (covering quite the range of grannies) on the site. Levy is asking for international submissions as well,

Seeking international submissions!

You can help promote this project by sharing the posts on your blog, Facebook wall, or by retweeting them.

The project has readers from more than 100 countries, but submissions from only a few.  Please help make this blog an international effort by submitting posts or encouraging others to post.

Call for submissions – short

Know any geeky grannies?  Seeking submissions for Grandma got STEM.  Email name+pic+story to [email protected]

Call for submissions – long

Call for submissions – Grandma got STEM.  Are you a grandmother working in a STEM (Science, Technology, Engineering, Mathematics) – related field?  Know any geeky grannies?  Email name+pic+story/remembrance to Rachel Levy:  ggstem (at) hmc (dot) edu.  Follow on Twitter: @mathcirque #ggstem  Project site:http://ggstem.wordpress.com

Presumably, the submissions need to be in English.

Getting back to Bittel’s Slate article, he mentions Foldit (here’s my first piece in an Aug. 6, 2010 posting [scroll down about 1/2 way]), a protein-folding game which has generated some very exciting science. He also notes some of that science was generated by older, ‘uneducated’ women. Bittel linked to Jeff Howe’s Feb. 27, 2012 article about Foldit and other crowdsourced science projects for Slate where I found this very intriguing bit,

“You’d think a Ph.D. in biochemistry would be very good at designing protein molecules,” says Zoran Popović, the University of Washington game designer behind Foldit. Not so. “Biochemists are good at other things. But Foldit requires a narrow, deeper expertise.”

Or as it turns out, more than one. Some gamers have a preternatural ability to recognize patterns, an innate form of spatial reasoning most of us lack. Others—often “grandmothers without a high school education,” says Popovic—exercise a particular social skill. “They’re good at getting people unstuck. They get them to approach the problem differently.” What big pharmaceutical company would have anticipated the need to hire uneducated grandmothers? (I know a few, if Eli Lilly HR is thinking of rejiggering its recruitment strategy.) [emphases mine]

There’s an interesting question and I didn’t see it answered in Howe’s article. What kind of grandmother who doesn’t have high school graduation joins a protein-folding game? I ask because neither of my parents had or have a high school education. Neither of them would have joined the game as neither would have had the confidence.

What I’ve tried to present here is a range of possibilities regarding age and education. Being older (female especially but also male, on occasion) doesn’t equal stupidity. As for education, I’ve never found that having high school graduation or a university degree(s) to be a guarantor of an exciting intellect. I mention these two points because it seems to me that people are being ranked as to age and education in ways that are unnecessarily exclusionary. Thank goodness for games like Foldit and websites like Grandma’s Got STEM which suggest alternatives to this relentless and ruthless form of ranking which disallows participation from the great bulk of us.

Visualizing nanotechnology data with Seed Media Group and GE (General Electric)

University of Washington (UW) researchers have uploaded a number of nanotechnology infographics on the visualizing.org website, from the UW Division of Design 2010: Nanotechnology Infographics webpage,

There are more than 1/2 dozen of these nanotechnology-themed infographics available on the page. This particular infographic, Nanotechnology:  Size Really is Everything,  has the following credit line,

By Kim Shedrick. Faculty: Karen Cheng, Marco Rolandi. Part of a series of infographics explaining nanotechnology through scale, how it has integrated into society, and what products it is being used in today.

Cheng and Rolandi have been mentioned here before in a Feb. 22, 2012 posting about their University of Washington Design Help Desk and their effort to match up scientists with designers in the interest of producing better science graphics.

I have nothing against better science graphics but I would like to know what information/data is supporting this and their other visualizations. I did resize the graphic to look more closely at the text but there were no references or citations.

Btw, The website handles ‘zooming’ in to see details clumsily. Rather than a click on the zooming tool resulting in a larger image, you are presented with an infographic which is now held within an Adobe PDF reader before you can magnify the image.

For those generally interested in infographics and visualizing date, there’s a lot to choose from on the Visualizing.org website. For those who like to dig a bit deeper, this site is a public relations ploy by General Electric and Seed Media Group. From the About Visualizing.org webpage,

Visualizing.org was created by GE and Seed Media Group to help make data visualization more accessible to the general public; to promote information literacy through the creation, sharing, and discussion of data visualizations; and to provide a unique resource to help simplify complex issues through design.

Seed Media seems to be an outgrowth (pun intended) of SEED Magazine. The magazine, which was founded by Adam Bly when he lived in Montréal, Canada, has always been focused on science and culture.  Headquarters for the magazine were moved to New York and, either at the same time or later, the magazine became a strictly online publication. From the Wikipedia essay (Note: Links have been removed),

Seed (subtitled Science Is Culture; originally Beneath the Surface) is an online science magazine published by Seed Media Group. The magazine looks at big ideas in science, important issues at the intersection of science and society, and the people driving global science culture. Seed was founded in Montreal by Adam Bly and the magazine is now headquartered in New York with bureaus around the world. May/June 2009 (Issue No. 22) was the last print issue. Content continues to be published on the website.

(I first mentioned SEED magazine in a Sept. 18, 2009 posting.) Interestingly, Seed Media which publishes the magazine makes no mention of it (that I could find) on its website. From Seed Media Group’s Learn webpage,

Scientific ThinkingTM

It’s a different way of looking at the world. It’s about using data to uncover patterns and design to confront complexity. It’s about connecting things to reveal systems. It’s about traversing scales and disregarding disciplines, applying neuroscience to economics, math to global health, virology to manufacturing, and genetics to law… It’s about experimenting all the way to understanding. It’s about changing your mind with new evidence – and getting as close to truth as humanly possible.

Getting 7 billion people to think scientifically has never been a small mission. And it has never been more important.

Since 2005, we have offered ideas and stories to help people think scientifically. Now we’re taking the next big step in this journey by creating tools and services to help institutions – companies, governments, and international organizations – do the same. We’re taking our way of seeing and thinking to parliaments, courtrooms, hospitals, construction sites, boardrooms… around the world – to catalyze scientific thinking at scale.

I’m not sure how one would go about trademarking ‘scientific thinking’ as this is  a very commonly used phrase and I’m pretty sure a case could be made that it has been common language for centuries.  This oddity had me going back to the Visualizing.org for their terms and conditions, which are largely unexceptionable,

These are the general terms of use. For terms and conditions regarding the uploading of work, please read the Visualization Submission Agreement.

This Web site is owned by General Electric Company (“GE”) and operated by Seed Media Group, LLC (“Seed”). Throughout the site, the terms “we,” “us” and “our” refer collectively to GE and Seed. We offer this Web site, including all information, tools and services available from this site, to you, the user, conditioned upon your acceptance of all the terms, conditions, policies and notices stated here. Your use of this site constitutes your agreement to these Terms of Use.

When you submit material other than a Visualization, you grant us and our affiliates an unrestricted, nonexclusive, royalty-free, perpetual, irrevocable and fully sublicensable right to use, reproduce, modify, adapt, publish, translate, create derivative works from, distribute and display such material throughout the world in any media. You further agree that we are free to use any ideas, concepts, know-how that you or individuals acting on your behalf provide to us. [emphasis mine] You grant us and our affiliates the right to use the name you submit in connection with such material, if we so choose. All personal information provided via this site will be handled in accordance with the site’s online Privacy Policy. You represent and warrant that you own or otherwise control all the rights to the content you post; that the content is accurate; that use of the content you supply does not violate any provision herein and will not cause injury to any person or entity; and that you will indemnify us for all claims resulting from content you supply.

Interesting, non? This has me wondering if it’s possible that  these folks (GE & Seed Media) might decide to use a concept from the visualization without any permission needed. If I understand this rightly, the promise is the visualization won’t be used, all they need is the idea or concept and either company (GE/Seed) or their affiliates can find someone else to illustrate or visualize it.  I find a company (Seed) that’s trying to trademark ‘scientific thinking’ might have some credibility issues regarding their stated terms and conditions for this visualizing.org website.

For the icing on this visualization cake, here’s a video from Visualizing.org’s About page where there is much discussion about the importance of design and visualization of data but not one single scientist is featured,

Memory chips could get organic and a nod to singer, Dean Martin

Researchers from the University of Washington (located in Washington state) and Southeast University (China) have found a way to create organic ferroelectric molecules which offer the possibility of flexible, nontoxic memory chips according a Jan. 24, 2013 news item on ScienceDaily,

At the heart of computing are tiny crystals that transmit and store digital information’s ones and zeroes. Today these are hard and brittle materials. But cheap, flexible, nontoxic organic molecules may play a role in the future of hardware.

A team led by the University of Washington in Seattle and the Southeast University in China discovered a molecule [diisopropylammonium bromide?] that shows promise as an organic alternative to today’s silicon-based semiconductors. The findings, published this week in the journal Science, display properties that make it well suited to a wide range of applications in memory, sensing and low-cost energy storage.

“This molecule is quite remarkable, with some of the key properties that are comparable with the most popular inorganic crystals,” said co-corresponding author Jiangyu Li, a UW associate professor of mechanical engineering.

The Jan. 24, 2013 University of Washington news release by Hannah Hickey, which originated the news item, details the advantages of these crystals while noting they are not likely to replace currently used ferroelectric materials as the new molecule is not suitable for all uses (Note: Links have been removed),

The carbon-based material could offer even cheaper ways to store digital information; provide a flexible, nontoxic material for medical sensors that would be implanted in the body; and create a less costly, lighter material to harvest energy from natural vibrations.

The new molecule is a ferroelectric, meaning it is positively charged on one side and negatively charged on the other, where the direction can be flipped by applying an electrical field. Synthetic ferroelectrics are now used in some displays, sensors and memory chips.

In the study the authors pitted their molecule against barium titanate, a long-known ferroelectric material that is a standard for performance. Barium titanate is a ceramic crystal and contains titanium; it has largely been replaced in industrial applications by better-performing but lead-containing alternatives.

The new molecule holds its own against the standard-bearer. It has a natural polarization, a measure of how strongly the molecules align to store information, of 23, compared to 26 for barium titanate. To Li’s knowledge this is the best organic ferroelectric discovered to date.

A recent study in Nature announced an organic ferroelectric that works at room temperature. By contrast, this molecule retains its properties up to 153 degrees Celsius (307 degrees F), even higher than for barium titanate.

The new molecule also offers a full bag of electric tricks. Its dielectric constant – a measure of how well it can store energy – is more than 10 times higher than for other organic ferroelectrics. And it’s also a good piezoelectric, meaning it’s efficient at converting movement into electricity, which is useful in sensors.

The new molecule is made from bromine, a natural element isolated from sea salt, mixed with carbon, hydrogen and nitrogen (its full name is diisopropylammonium bromide). Researchers dissolved the elements in water and evaporated the liquid to grow the crystal. Because the molecule contains carbon, it is organic, and pivoting chemical bonds allow it to flex.

The molecule would not replace current inorganic materials, Li said, but it could be used in applications where cost, ease of manufacturing, weight, flexibility and toxicity are important.

Here’s a citation and link to the paper,

Diisopropylammonium Bromide Is a High-Temperature Molecular Ferroelectric Crystal by Da-Wei Fu, Hong-Ling Ci, Yuanming Liu, Qiong Ye, Wen Zhang, Yi Zhang, Xue-Yuan Chen, Gianluca Giovannetti, Massimo Capone, Jiangyu Li, Ren-Gen Xiong. Science 25 January 2013:
Vol. 339 no. 6118 pp. 425-428. DOI: 10.1126/science.1229675

This paper, along with a few others about ferroelectric materials in the Jan. 2013 issue of Science, is behind a paywall. Given the title of the paper, I’ve made the assumption that the new molecule is diisopropylammonium bromide.

At any rate, all of this has led me to an old song by singer, Dean Martin, titled ‘Memories are made of this,’

I found this piece of information in the comments,

 neuro518 3 weeks ago

the guitarist is Terry Gilkyson and his group here is called the Easy Riders. He wrote this song and hundreds of others including “Fast Freight” performed by the Kingston Trio. He was in at the very beginning of the transition of American music from pop to folk and was one of the best. For some reason he never gets much credit, but he was one of the best.

Happy Friday, Jan. 25, 2013.

Are we and our world a computer simulation?

There is a fascinating Dec. 10, 2012 news item on Nanowerk about a philosophical question that’s being researched by a team of physicists at the University of Washington (Note: I have removed a link),

The concept that current humanity could possibly be living in a computer simulation comes from a 2003 paper published in Philosophical Quarterly (“Are You Living In a Computer Simulation?“) by Nick Bostrom, a philosophy professor at the University of Oxford. In the paper, he argued that at least one of three possibilities is true:

The human species is likely to go extinct before reaching a “posthuman” stage.

Any posthuman civilization is very unlikely to run a significant number of simulations of its evolutionary history.

We are almost certainly living in a computer simulation.

He also held that “the belief that there is a significant chance that we will one day become posthumans who run ancestor simulations is false, unless we are currently living in a simulation.”

Here’s what the University of Washington physicists, from the Dec. 10, 2012 University of Washington news release by Vincent Stricherz, which originated the news item,

With current limitations and trends in computing, it will be decades before researchers will be able to run even primitive simulations of the universe. But the UW team has suggested tests that can be performed now, or in the near future, that are sensitive to constraints imposed on future simulations by limited resources.

Currently, supercomputers using a technique called lattice quantum chromodynamics and starting from the fundamental physical laws that govern the universe can simulate only a very small portion of the universe, on the scale of one 100-trillionth of a meter, a little larger than the nucleus of an atom, said Martin Savage, a UW physics professor.

However, Savage said, there are signatures of resource constraints in present-day simulations that are likely to exist as well in simulations in the distant future, including the imprint of an underlying lattice if one is used to model the space-time continuum.

The supercomputers performing lattice quantum chromodynamics calculations essentially divide space-time into a four-dimensional grid. That allows researchers to examine what is called the strong force, one of the four fundamental forces of nature and the one that binds subatomic particles called quarks and gluons together into neutrons and protons at the core of atoms.

“If you make the simulations big enough, something like our universe should emerge,” Savage said. Then it would be a matter of looking for a “signature” in our universe that has an analog in the current small-scale simulations.

Savage and colleagues Silas Beane of the University of New Hampshire, who collaborated while at the UW’s Institute for Nuclear Theory, and Zohreh Davoudi, a UW physics graduate student, suggest that the signature could show up as a limitation in the energy of cosmic rays.

In a paper they have posted on arXiv, an online archive for preprints of scientific papers in a number of fields, including physics, they say that the highest-energy cosmic rays would not travel along the edges of the lattice in the model but would travel diagonally, and they would not interact equally in all directions as they otherwise would be expected to do.

“This is the first testable signature of such an idea,” Savage said.

If such a concept turned out to be reality, it would raise other possibilities as well. For example, Davoudi suggests that if our universe is a simulation, then those running it could be running other simulations as well, essentially creating other universes parallel to our own.

“Then the question is, ‘Can you communicate with those other universes if they are running on the same platform?’” she said. [emphasis mine]

Here’s the citation for and a link to the arXiv.org paper by Beane, Davoudi, and Savage,

Constraints on the Universe as a Numerical Simulation by Silas R. Beane, Zohreh Davoudi, Martin J. Savage (Submitted on 4 Oct 2012 (v1), last revised 9 Nov 2012 (this version, v2))

Fascinating, yes?

Contraception and HIV protection in cloth*

Researchers at the University of Washington have published a study in the peer-reviewed, open access journal, Public Library of Science ONE (PLoS ONE), concerning their work to produce fibres that can deliver both contraceptives and anti-HIV drugs, according to a Nov. 30, 2012 news item on Nanowerk,

The only way to protect against HIV and unintended pregnancy today is the condom. It’s an effective technology, but not appropriate or popular in all situations.

A University of Washington team has developed a versatile platform to simultaneously offer contraception and prevent HIV. Electrically spun cloth with nanometer-sized fibers can dissolve to release drugs, providing a platform for cheap, discrete and reversible protection.

Hannah Hickey’s  Nov. 30, 2012 University of Washington news release, which originated the news item, provides details,

“Our dream is to create a product women can use to protect themselves from HIV infection and unintended pregnancy,” said corresponding author Kim Woodrow, a UW assistant professor of bioengineering. “We have the drugs to do that. It’s really about delivering them in a way that makes them more potent, and allows a woman to want to use it.”

Electrospinning uses an electric field to catapult a charged fluid jet through air to create very fine, nanometer-scale fibers. The fibers can be manipulated to control the material’s solubility, strength and even geometry. Because of this versatility, fibers may be better at delivering medicine than existing technologies such as gels, tablets or pills. No high temperatures are involved, so the method is suitable for heat-sensitive molecules. The fabric can also incorporate large molecules, such as proteins and antibodies, that are hard to deliver through other methods.

They first dissolved polymers approved by the Food and Drug Administration and antiretroviral drugs used to treat HIV to create a gooey solution that passes through a syringe. As the stream encounters the electric field it stretches to create thin fibers measuring 100 to several thousand nanometers that whip through the air and eventually stick to a collecting plate (one nanometer is about one 25-millionth of an inch). The final material is a stretchy fabric that can physically block sperm or release chemical contraceptives and antivirals.

“This method allows controlled release of multiple compounds,” Ball said. “We were able to tune the fibers to have different release properties.”

One of the fabrics they made dissolves within minutes, potentially offering users immediate, discrete protection against unwanted pregnancy and sexually transmitted diseases.

Another dissolves gradually over a few days, providing an option for sustained delivery, more like the birth-control pill,  to provide contraception and guard against HIV.

The fabric could incorporate many fibers to guard against many different sexually transmitted infections, or include more than one anti-HIV drug to protect against drug-resistant strains (and discourage drug-resistant strains from emerging). Mixed fibers could be designed to release drugs at different times to increase their potency, like the prime-boost method used in vaccines.

The electrospun cloth could be inserted directly in the body or be used as a coating on vaginal rings or other products.

Electrospinning has existed for decades, but it’s only recently been automated to make it practical for applications such as filtration and tissue engineering. This is the first study to use nanofibers for vaginal drug delivery.

While this technology is more discrete than a condom, and potentially more versatile than pills or plastic or rubber devices, researchers say there is no single right answer.

The citation and link to the article,

Drug-Eluting Fibers for HIV-1 Inhibition and Contraception by Cameron Ball, Emily Krogstad, Thanyanan Chaowanachan, Kim A. Woodrow (2012) PLoS ONE 7(11): e49792. doi:10.1371/journal.pone.0049792

Last month, the Bill and Melinda Gates Foundation awarded these researchers a $1M grant to pursue this work.

*ETA Dec.2.12: I erroneously used the word clothing in the headline. It’s now been corrected to ‘cloth’.

Canadian scientists get more light in deal with the US Argonne National Laboratory

Canada’s synchrotron, Canadian Light Source (based in Saskatchewan), has signed a new three-year deal with the US Dept. of Energy’s Argonne National Laboratory’s Advanced Photon Source (APS)  that will give Canadian scientists more access to the APS facilities, according to the June 18, 2012 news item at the  Nanowerk website,

Seeking to solve some of today’s greatest global problems, scientists using x-ray light source facilities at national research laboratories in the United States and Canada are sharing more expertise.

The Canadian Light Source (CLS) and the Advanced Photon Source (APS) at the U.S. Department of Energy’s (DOE’s) Argonne National Laboratory agreed in January 2012 to a Partner User Proposal that cements a stronger working relationship between the two facilities for the next three years. These two premier light sources use different but complementary x-ray techniques to probe materials in order to understand chemical and structural behavior.

Tone Kunz’s June 18, 2012 news release for the APS provides details about the deal,

This new agreement will provide Canadian scientists with more research time to use the x-ray light source facilities and more time on a larger number of APS beamlines. Using varied x-ray and imaging capabilities will broaden the range of experiments Canadians may undertake at the APS to augment their research done at the Canadian Light Source. X-ray science offers potential solutions to a broad range of problems in surface, material, environmental and earth sciences, condensed matter physics, chemistry, and geosciences.

Since the Sector 20 beamlines became fully operational, scientists from Canada and other areas who have used these beamlines at the APS have produced an average of 51 scientific publications a year. This research includes the study of more effective mineral exploration strategies, ways to mitigate mine waste and mercury contamination, and novel ways to fabricate nanomaterials for use in fuel cells, batteries, and LEDs.

I had not realized how longstanding the  CLS/APS relationship has been,

Before the Canadian Light Source began operation in 2004, a Canadian group led by Daryl Crozier of Simon Fraser University, working in partnership with colleagues at the University of Washington and the Pacific Northwest National Laboratory, helped found the Sector 20 beamlines at the APS as part of the Pacific Northwest Consortium Collaborative Access Team, or PNC-CAT. Parts of this team were included in the X-ray Science Division of the APS when it was formed.

This long-standing partnership has led to scientifically significant upgrades to the beamline. The new agreement will provide the valuable manpower and expertise to allow the APS to continue to push the innovation envelope. [emphasis mine]

As I was reading Kunz’s news release I kept asking, what’s in it for the APS? Apparently they need more “manpower and expertise.” Unfortunately, their future plans are a little shy of detail,

Scientists from the APS and the Canadian Light Source will work together on R&D projects to improve light-source technology. In particular, scientists will upgrade even further the two beamlines at Sector 20 in four key areas. This will provide a unique capability to prepare and measure in situ films and interfaces, a new technique to create quantitative three-dimensional chemical maps of samples, and improved forms of spectroscopy to expand the range of elements and types of environments that can be examined.

What are the four key areas? For that matter, what is Sector 20? I suspect some of my readers have similar questions about my postings. It’s easy (especially if you write frequently) to forget that your readers may not be as familiar as you are with the subject matter.

(I wrote about the CLS and another deal with a synchrotron in the UK in my May 31, 2011 posting.)

Science images too busy/ugly? Call the University of Washington’s Design Help Desk

After several days at the AAAS (American Association for the Advancement of Science) 2012 annual meeting, I can definitely support the design help desk project at the University of Washington (UW). From the Feb. 22, 2012 news item by Hannah Hickey on physorg.com,

A group of University of Washington researchers has launched a unique experiment matching science students with those in design. The new Design Help Desk, similar to a writing help desk, offers scientists a chance to meet with someone who can help them create more effective figures, tables and graphs.

“In modern publications, up to half of the space can be taken up by figures,” said principal investigator Marco Rolandi, a UW assistant professor of materials science and engineering. His group studies materials at the nanometer scale, and much of the data is ultimately contained in microscope images.

“As a new faculty member, I was spending a lot of time teaching my students how to make figures for publications, even though I myself didn’t have any formal training,” Rolandi said.

It was a case of the blind leading the blind, he said. Rolandi sought out collaborators on campus, and eventually funding from the National Science Foundation, to create support that until now didn’t exist – and to study how well it works.

The research project (Design Help Desk) has two principal investigators, Rolandi and Karen Cheng, from Hickey’s Feb. 21, 2012 news release on the University of Washington website,

“We are becoming a more visual culture,” says Karen Cheng, a UW associate professor of design (who also completed a bachelor’s in chemical engineering). Still, most science visuals “could use significant improvement from a visual point of view,” she said. “It’s just not a field where design has been part of the training.”

This hasn’t always been the case. In Galileo’s time, scientists were also trained in art. These days, scientists often produce a graph using Microsoft Excel or PowerPoint’s default settings – which might look fine to them, but may have fundamental design problems. [emphasis mine]

Meanwhile, even journals are focusing on the importance of figures, often asking authors to improve them before publication.

“It’s not just about looking pretty. It’s about conveying complex information in a clear way,” Cheng said.

The point about science and art being more closely intertwined in the past was made Gunalan Nadarajan (Vice Provost at the Maryland Institute College of Art) at the AAAS 2012 annual meeting (my Feb. 20, 2012 posting). Nadarajan mentioned a new project being developed, Network for Science Engineering Art and Design. It’s so new they don’t yet have a website.

This is not being done in the wild. Scientists and designers are not set loose upon each other (from the UW news release),

Clients who arrive for a session at the Design Help Desk are first greeted by postdoctoral researcher Yeechi Chen, who earned her doctorate in physics at the UW and has completed a UW certificate course in natural science illustration. Chen can act as an intermediary between the scientist and the designer, and reassure new clients that scientists are involved in the project.

During the half-hour session, the scientist client and design consultant are alone in the room. The designer first asks the scientist about his or her goals – timeline, stage in the design process, publication venue, and main points to convey. The designers typically use pen and paper to sketch out their ideas.

The session is videotaped for use in the group’s study, if the client agrees. One camera records the face-to-face interaction, while a second camera on the ceiling records the sketching and hand movements.

Interestingly (to me anyway), the Design Help Desk appears on a UW webpage dedicated to Visual Communication in {Nano} Science. The page offers a very minimalist image, a description of the project and the team, and offers links to resources, e.g., A Brief Guide to Designing Effective Figures for the Scientific Paper ((behind a paywall)) which was published  in August 2011 in Advanced Materials.

Step closer to integrating electronics into the body

The Sept. 20, 2011 news item (Proton-based transistor could let machines communicate with living things) on Nanowerk features a rather interesting development,

Human devices, from light bulbs to iPods, send information using electrons. Human bodies and all other living things, on the other hand, send signals and perform work using ions or protons.

Materials scientists at the University of Washington have built a novel transistor that uses protons, creating a key piece for devices that can communicate directly with living things.

Here’s a diagram from the University of Washington Sept. 20, 2011 article about the proton transistor by Hannah Hickey,

 

On the left is a colored photo of the UW device overlaid on a graphic of the other components. On the right is a magnified image of the chitosan fibers. The white scale bar is 200 nanometers. (Marco Rolandi, UW)

Here’s a little more about the proton transistor (from the Hickey article),

In the body, protons activate “on” and “off” switches and are key players in biological energy transfer. Ions open and close channels in the cell membrane to pump things in and out of the cell. Animals including humans use ions to flex their muscles and transmit brain signals. A machine that was compatible with a living system in this way could, in the short term, monitor such processes. Someday it could generate proton currents to control certain functions directly.

A first step toward this type of control is a transistor that can send pulses of proton current. The prototype device is a field-effect transistor, a basic type of transistor that includes a gate, a drain and a source terminal for the current. The UW prototype is the first such device to use protons. It measures about 5 microns wide, roughly a twentieth the width of a human hair.

As for the device (from the Hickey article),

The device uses a modified form of the compound chitosan originally extracted from squid pen, a structure that survives from when squids had shells. The material is compatible with living things, is easily manufactured, and can be recycled from crab shells and squid pen discarded by the food industry.

There is a minor Canadian connection,

Computer models of charge transport developed by co-authors M.P. Anantram, a UW professor of electrical engineering, and Anita Fadavi Roudsari at Canada’s University of Waterloo, were a good match for the experimental results.

If I understand this correctly, the computer models were confirmed by the experimental  results, which means the computer models can be used (to augment the use of expensive experiments) with a fair degree of confidence.

I am finding this integration of electronics into the body both fascinating and disturbing as per my paper, Whose electric brain? More about that when I have more time.

A*STAR and University of Washington joint optoelectronics project

At the University of Washington located in Seattle, a joint project with A*STAR, Singapore’s Agency for Science, Technology and Research is about to get underway. From the Sept. 16, 2011 news item on Nanowerk,

A*STAR Institute of Microelectronics (IME) and the University of Washington announce that they will join forces to provide shared Silicon Photonics processes as part of the Optoelectronics Systems Integration in Silicon programme (OpSIS). This will help the research and development (R&D) community significantly reduce the fabrication cost of silicon photonics integrated circuits.

The silicon photonics integrated circuits to be created under this programme will be immediately available to the photonic research community worldwide, and in the process, facilitate technological advancements and proliferate creative ideas for the development of the next generation devices. As the platform will be offered through multi-project wafer (MPW) runs, which allow users from multiple projects to share the costs of a single fabrication run, research costs are lowered significantly for individual projects.

More information at A*STAR’s Institute of Microeletronics (IME) can be found here and about the University of Washington’s OpSIS programme here.