96,000 Square Miles » Library http://www.ohsu.edu/blogs/96kmiles Sat, 24 Jun 2017 00:11:19 +0000 en-US hourly 1 http://wordpress.org/?v=4.2.15 The heart of the university http://www.ohsu.edu/blogs/96kmiles/2012/12/21/ohsu-library-information/ http://www.ohsu.edu/blogs/96kmiles/2012/12/21/ohsu-library-information/#comments Fri, 21 Dec 2012 16:00:37 +0000 http://www.ohsu.edu/blogs/96kmiles/?p=359 Read More]]> Written by Jackie Wirz, Ph.D.

“I have always imagined that Paradise will be a kind of library” – Jorge Luis Borges

Jorge Luis Borges was an influential Spanish American novelist, perhaps best known for his inventive short stories.  His quotes have sparked literally thousands of essays by hopeful library students, much like the “two paths diverged in the woods” cliché for personal statement essays (see previous blog post here).

Although I admire this quote and agree with it on many levels, my favorite library quote comes from legendary fashion designer Karl Lagerfeld. In addition to being the creative force behind the House of Chanel, he also owns an impressive library and a bookstore. According to Karl, “Books are a hardbound drug with no danger of overdose. I am a happy victim of books.”

OK, perhaps equating books to drugs at a medical campus is not the best course of action, but my major point here is that books have been and continue to be a passion for me.

Is that why I work at a library? The honest answer to that is no. Although our collection of books is extensive and lovely, I hold a burning desire to read only a select few of them. Principles of Physical Biochemistry is a personal favorite, and I’d recommend The Elements of Style to pretty much everybody. Despite my geekiness, I am not remotely interested in reading (or even looking through) the The Color Atlas and Synopsis of Clinical Dermatology  or Dental Caries : the Disease and its Clinical Management.  In short, books are not the reason I work at the library.

Yes, I can practically hear you thinking right now, “Aren’t books the heart of the library?” And for many institutions and libraries across the nation, books do form the cornerstone of a library.

However, the OHSU Library, like many academic research libraries, carries a diverse cross section of information in a variety of shapes and forms: for example, we have an extensive historical collection of medical artifacts, a collection of oral histories, thousands of journals and hundreds of databases.  Some of these items are digital and only a sub-section of them are bound in book format.

The heart of the library could be considered to be the wealth of information in all of its glorious manifestations.

But even here I would disagree. I work at a library because I believe that the heart of the library is contained in the people who work here. Our jobs are not only to ensure that OHSU faculty, students, staff and Oregonians everywhere have access to information; we are also entrusted with facilitating the educational, outreach and research mission of OHSU.

From our amazing Nursing Librarian Loree Hyde to our entire administrative staff, from our brand new Digital Collections Librarian Kyle Banerjee to our long-standing circulation team, each and every individual in the library performs above and beyond the call of duty to help us all find and manage the information we need to succeed as a university. We all have a passion for what we do, and working with these amazing people is what makes this library my home.

Taking it one step further, I also agree with former Harvard President Charles W. Eliot: “The Library is the heart of the University.”

In my opinion, it is the people that make the heart of the library, and these are just some of the same people that make the vibrant heart of  OHSU.

***

Jackie Wirz is an Assistant Professor and the Biomedical Sciences Information Specialist at the Oregon Health & Science University Library. She earned her Ph.D. from Oregon Health & Science University in Biochemistry & Molecular Biology and has a B.S. from Oregon State University in Biochemistry & Biophysics. Her research career has spanned 15 years and has covered diverse topics such as transcriptional regulation, macromolecular structure determination, collagen biophysics and DNA repair. Her professional interests include information, data, and knowledge management, as well as the publishing paradigms of scientists.

Additionally, Jackie is a strong proponent of science outreach and volunteers with a variety of programs designed to promote scientific literacy. Jackie believes in evolution, salted caramel buttercream and Jane Eyre.

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Must-read: “The DNA Book” http://www.ohsu.edu/blogs/96kmiles/2012/10/10/must-read-the-dna-book/ http://www.ohsu.edu/blogs/96kmiles/2012/10/10/must-read-the-dna-book/#comments Wed, 10 Oct 2012 20:24:39 +0000 http://www.ohsu.edu/blogs/96kmiles/?p=243 Read More]]> Written by Jackie Wirz, Ph.D.

What’s on your must-read list?

High on mine is Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves by Harvard professor George Church. It hit shelves in the traditional paper and ink format on Tuesday, Oct. 2. Yet Dr. Church has carried billions of copies of his book stored in a small test tube that he carries around in his pocket since last spring.

How is this possible? Dr. Church and his research team at Harvard recently converted the 53,000 word book into DNA. And it wasn’t just words that made the jump from text to genetic storage—the researchers encoded 11 images and even a computer program in their book, making this ambitious project the largest and most complex use of DNA as an artificial storage medium to date.

DNA is, of course, capable of storing complex information such as the instructions to create an entire human being.  No small task, considering that it consists of only four bases: adenine (A), guanine (G), cytosine(C) and thymine (T).

DNA has several unique advantages as a data platform, most importantly its capacity to be an incredibly dense storage system. Unlike traditional mechanisms of storage which are confined to two dimensions, DNA can store information in glorious 3D. The authors of the DNA Book compared different technologies for encoding data, converting the information into volumetric data densities; although traditional data is encoded in 2D along a flat surface, a CD (for example) still has thickness, which was used in the volumetric calculations. A commercial CD contains roughly 413,000 bits per cubic mm. In contrast, the purified DNA book produced by Church and colleagues is stored at an astonishing 5.49 x 1015 bits per cubic mm.

Put another way, if that CD was made of three dimensionally encoded DNA, you could store 13 billion albums on one DNA disc.  Not too shabby!

DNA is also extremely durable. When purified or properly preserved, it can survive for thousands of years unharmed (Remember that part of Jurassic Park where they extract DNA from amber-coated fossils?  Totally true!). It is stable at a variety of temperatures, and is biologically suited to be a long lasting storage medium. The fundamental tools necessary to work with DNA are literally encoded in all of nature; it doesn’t take long for our technology to outstrip and outdate our storage media (Jazz drives anybody?), but the enzymes and chemicals necessary to work with DNA are literally carried within most organisms on this planet.

That isn’t to say, however, that current DNA technology is user-friendly. Although the scientists in this study were careful to use “off the shelf” technology to create and sequence their DNA book, they are still professional scientists with training and equipment expertise in DNA manipulation. Even more of a hurdle is the expense: DNA synthesis and sequencing is still expensive and not commercially available to the average Joe.

But the times, they are a changing. Remember the hullabaloo surrounding the human genome project? Initiated in 1990, it took $3 billion dollars and 13 years to sequence the first human genome (however, this cost also included scientific activities related to genomics – the human genome sequencing was only a fraction of the overall budget). Now, it is estimated that the cost to sequence a genome hovers around $7500 dollars, and dropping rapidly. Perhaps DNA as a storage medium is closer to affordable than you may think.

But exactly how close are we to a sci-fi future? The idea that we’d be able to swallow a DNA copy of the Encyclopedia Britannica and suddenly have the information embedded in us is still wrong. Yes, the entire encyclopedia can be encoded in DNA, but if we ate it our body would just digest it.

We could theoretically create and infect ourselves with an Encyclopedia Britannica virus (e. britannicus), but it wouldn’t mean very much since the body’s mechanism of “reading” DNA is different than the technique used by the DNA Book researchers. In fact, DNA as an ideal storage medium works best when there are no living organisms involved—a fact acknowledged by the Harvard research team. The biological function of our natural cells could be disrupted or even damaged, the information is much less stable in living ecosystems and there would be a constant problem with DNA degradation or mutation (practically a non-issue when DNA is purified and stored on a microchip). So don’t hope to have an Encyclopedia Britannica add-on tacked to your genes any time soon.

Even though Church’s book can be easily copied and distributed (they considered including a DNA copy with every print edition of the book, but decided against it), the cost of reading the information with a DNA sequencer remains too rich for everyday use. For the time being, your best mechanism for checking out the Encyclopedia Britannica will still involve a trip to your local library. Stop on by—we’d be happy to help you learn more about DNA technology, sequencing and data management and storage. We may be using those old fashioned print books to help you out, but sometimes it’s nice having a book in your hand rather than a test tube of DNA.

***

Jackie Wirz is an Assistant Professor and the Biomedical Sciences Information Specialist at the Oregon Health & Science University Library. She earned her Ph.D. from Oregon Health & Science University in Biochemistry & Molecular Biology and has a B.S. from Oregon State University in Biochemistry & Biophysics. Her research career has spanned 15 years and has covered diverse topics such as transcriptional regulation, macromolecular structure determination, collagen biophysics and DNA repair. Her professional interests include information, data, and knowledge management, as well as the publishing paradigms of scientists.

Additionally, Jackie is a strong proponent of science outreach and volunteers with a variety of programs designed to promote scientific literacy. Jackie believes in evolution, salted caramel buttercream and Jane Eyre.

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Heartbreaking works of staggering genius http://www.ohsu.edu/blogs/96kmiles/2012/06/13/heartbreaking-works-of-staggering-genius/ http://www.ohsu.edu/blogs/96kmiles/2012/06/13/heartbreaking-works-of-staggering-genius/#comments Wed, 13 Jun 2012 23:05:46 +0000 http://www.ohsu.edu/blogs/96kmiles/?p=32 Read More]]>

Jackie Wirz, Ph.D., assistant professor and biomedical sciences information specialist, OHSU Library

By Jackie Wirz, Ph.D.

Hello there – my name is Jackie, and I am the Biomedical Science Specialist and Assistant Professor at the OHSU Library.  Sounds pretty impressive, doesn’t it?  I have fancy business cards and everything.  But I have a secret to tell – I was actually a graduate student here at OHSU.  As such, I know all of the places to get food at 2 a.m., the warmest areas to catch a nap between time points, places with showers when you’ve been at work for 24 or more hours straight, and how to get to all of the major seminar rooms on campus indoors.  Despite my many (many!) years in student mode, I am sad to say that one place I seldom set foot in was the OHSU Library.  It’s not that I didn’t use their resources – every day I accessed the many electronic journals and databases that the Library provides – I just didn’t physically enter the Library very often.

Hmmm, I’m not starting this column about the Library very well…  I could spend time on this, my first blog post, to advertise our extensive collection – our thousands of journals, hundreds of databases, amazing staff, etc., but I’ll get to that some other time.  Today I’d like to discuss what I consider to be the most unique and valuable resources in the Library: the student theses and dissertations.  When I did venture to the Library as a student, I would oftentimes swing by this area of the collection (also known as the “Wall of Wisdom,” the “Shelves of Scholarship” and the “Blue Light Special” since a majority of the titles are hardbound in shades of blue).  This area houses all of the student theses and dissertations from all of our graduate programs from 1994 to the present (older volumes are in storage).  It’s an impressive array of topics, ranging from dietetics to structural biology, public health to biomedical informatics.

As a student, I would approach the wall with mixed feelings.  Sometimes I would look at the collected works and despair for my project – would I ever be able to compile my strings of failed experiments into an organized, cohesive work?  Much less one that was longer than 20 pages?  At other times I would be inspired by the impressive work that was produced by my peers, especially some amazing theses from my department (Martha Sommer and Ezhilkani Subbian, represent).  Now that my own meager contribution lies on the “Shelves of Scholarship,” I feel that I can look at these collected works with a little more perspective.  If you look beyond the citations, published chapters and research plans, you can begin to read between the lines.  You will find that each of these theses represents more than the intellectual growth of the next generation of medical professionals; more than a chapter in a professional life; more than the sum of its parts – hidden in these pages are stories of personality, perseverance, redemption, loss, humor…  In every volume you will find testament to the hard work and dedication that underpins any graduate career.  Moreover, you will find all of the reasons that make our time here at OHSU not just a place of learning, but a place of growth.

Our theses and dissertations don’t get as much use as our institutional subscriptions to Science or Dynamed, but the contents within those blue bound pages are more intensely personal to our community than you may think.  This area in the Library is one that I now pass on a daily basis, and it serves as a reminder to me that our output of research is so much more than a citation.  I may not have appreciated this enough as a student, but now that I work at the Library, I feel strongly that these works of staggering genius should be shared.  They are truly unique items in our collection, and ones that are well worth seeing.  I hope you drop by and peruse our “Wall of Wisdom” – I think you’ll be inspired by our amazing student population.

***

Jackie Wirz is an Assistant Professor and the Biomedical Sciences Information Specialist at the Oregon Health & Science University Library. She earned her Ph.D. from Oregon Health & Science University in Biochemistry & Molecular Biology and has a B.S. from Oregon State University in Biochemistry & Biophysics. Her research career has spanned 15 years and has covered diverse topics such as transcriptional regulation, macromolecular structure determination, collagen biophysics and DNA repair. Her professional interests include information, data, and knowledge management, as well as the publishing paradigms of scientists. Additionally, Jackie is a strong proponent of science outreach and volunteers with a variety of programs designed to promote scientific literacy.  Jackie believes in evolution, salted caramel buttercream and Jane Eyre.

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