Discovering Biology in a Digital World

Could an iTunes-like model work with scientific publishing?

Tue, 10 Jan 2012 12:11:53 -0500

Many of you may remember a time when music-stealing was rampant on the internet.  Apple changed this situation by establishing a new kind of marketplace.  Now people pay for music and download it from iTunes.What if there were a third party group, with an iTunes-like model, where scientific publishers would make papers available for purchase? Could this kind of model work?Two arguments support this idea.1.  Volume sales2.  The cost of creationVolume salesVolume sales work like this.  Let's say a publisher sells 10 papers at $30 each.  This brings in $300.That same publisher could also bring in $300 by selling 100 papers at $3 each.  They could earn the same of money but get materials out to more people.Will the volume be there?  The experiment hasn't been tried.The cost of creationMany people have noted that most of the cost of creating a scientific publication is funded by taxpayers through government grants. The recording industry lacks that support, yet it seems to have survived the iTunes pricing model.I made a table below that compares some aspects of the recording industry with scientific publishing  (you can click the image to see a larger version).Granted recording artists and scientists, and their funding sources have different goals.  In the case of the scientific research the goal is to advance knowledge.  One would assume that access to knowledge is an important part of making this work.One of our commenters noted that paying $30 a paper, is hardship for many.  Not only does this obstacle discourage students from using scientific literature, it prevents the public from accessing peer-reviewed work. It does seem that the taxpayers who fund most of this work should get a better return on their investment.Another commenter volunteered that journal pricing practices aren't a problem because he could use his MIT and Harvard logins to get papers. Certainly, a system where small companies and individuals rely on friends with library subscriptions is one way to get papers, but wouldn't a system that's less dishonest be a better one? Read the comments on this post...[...]

How much does it cost to get a scientific paper?

Mon, 09 Jan 2012 13:19:25 -0500

The Backstory:  As it stands today,when one of the National Institutes of Health (NIH) provides the funding for a scientific research project, and those results are published, they must be made freely available to public, within a set period of time.  The reasoning behind this requirement is that taxpayers funded everything about the research except for the final publication, and so they have already paid for access.The Research Works Act (#RWA), HR 3699, is a bill in the House of Representatives that would roll back this requirement.  If it passes, taxpayers will most likely have to pay exorbitant fees for access to publicly-funded research.  I'll explain why in a moment.The Research Works Act will harm science education because students and instructors at small colleges and community colleges generally lack access to scientific journals and we will no longer be able to afford to use scientific literature in our courses.How much does it cost? One commenter on a my earlier post about the effect on science education noted that students and others would still be able to purchase research articles if RWA passes.I thought, dear readers, you might like to know what that privilege is likely to cost. What does a personal subscription cost today?Today, a one year personal subscription to Science costs $149 for a member and $75 for a student. A personal subscription for one year of Nature costs $199.  We subscribe to both and pay $350 a year for the privilege.The problem is that working in science, and learning about science, requires looking at papers from multiple journals and multiple years from those journals.Access to one journal is rarely sufficient.Let's look at the subscription costs for some other journals.Two other journals that I frequently use are Nature Genetics and Nature Biotechnology. These cost $225 per year and $250 per year, respectively. Here are the yearly subscription costs for a few of the other Nature journals: $503  Acta Pharmacologica Sinica $586  American Journal of Hypertension $319  Asian Journal of Andrology $865  Bone Marrow Transplantation $99    BoneKEy Reports $474  British Dental Journal $569  British Journal of Cancer $542  Cancer Gene Therapy $417  Cell Death and Differentiation $417  Cell Research At $865 per year, a personal subscription to the on-line only version, of Bone Marrow Transplantation would be hard for me to justify.  But then, I'm not an M.D. Now, consider Nature has 91 publications, with many subscription costs over $300 per year for each journal. I've been told that library subscriptions are more costly than personal subscriptions.  Is it really that surprising that our libraries say no? What do individual articles cost?Could we get by with having students read individual articles? I looked up the prices for individual articles from some of the journals that I use. The table below shows the costs to purchase a single article from 14 different journals. Out the 14 journals, 9 of them charge $30 per article or more. I looked at multiple Nature journals since the prices for each journal subscription varied so widely.  Many times when we have students research a topic, we want them to look at multiple articles from multiple journals. Students might need to look at ten papers to complete an assignment.We also tend to have students investigate different topics.  This means that we can't just give every student the same set of articles.  Each student needs to get multiple articles from multiple sources, and each article could cost $30-35 at today's prices.  Today, we can make do by having students stick to open access articles. RWA will kill that option. If papers were priced more reasonably, like songs in iTunes, we instructors would find RWA less alarming.  But as it stands, if publishers charge the all articles with the prices they're using now, it will kill our ability to use the literature in [...]

Learn how to use scientific articles in education at the C.R.E.A.T.E. June workshop

Fri, 06 Jan 2012 19:05:01 -0500

The C.R.E.A.T.E. strategy is an approach to making biology teaching a better model of biology, the science.

From the C.R.E.A.T.E website,

...C.R.E.A.T.E. teaching focuses on on authentic published work--peer reviewed journal articles--with students reading either series of papers produced sequentially from individual labs or series of papers from different labs focused on a single line of research.

This summer and next, the National Science Foundation is funding two identical workshops designed to help instructors learn how to use the C.R.E.A.T.E. strategy.

These will be held in June 2012 and 2013 at Hobart College and William Smith College, in Geneva, New York. All expenses will be covered except for travel.

If you're interested, APPLY NOW The deadline is January 15, 2012.

You can download the pdf application form and more information from this page.

C.R.E.A.T.E. stands for:

Consider
Read
Elucidate the hypotheses
Analyze and interpret the data and
Think of the next
Experiment

The timing of the workshop announcement a little ironic, since New York congresswoman Carolyn Maloney is co-sponsoring a bill (HR3699 The Research Works Act (click the "Bill pdf" link at the site to download the bill) that will make it much more difficult for students to access this valuable resource.

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Raising the barriers: restricting access to scientific literature will hurt STEM education

Fri, 06 Jan 2012 17:10:45 -0500

This morning, I learned that congress wants to reverse the advances made by NIH and go back to restricting access to scientific publications. Congresswoman Carolyn Maloney (New York) and Congressman Darrell Issa (California) are co-sponsoring a bill to restore the limits on public access to NIH-funded research. I've written many times before (here, here, here, and here) about the challenges that community college faculty and students have in getting access to scientific papers. In an era where the economic benefits of educating students in science are well-known (1), the idea of crippling science education by cutting off access to the primary literature is puzzling. If anything, I would expect congress to support science education by asking the National Science Foundation (NSF) to follow NIH's lead and require that publications from NSF funded research be made open access, too. Instead, bill H.R. 3699 will roll back the NIH Public Access Policy and block similar policies at other federal agencies. The effects would be horrific.  Maloney and Issa might not be aware of this, but faculty and students at 1,167 community and technical colleges will be negatively impacted by this bill (2). Many community college faculty rely on open access materials. Not only are these publications important tools for keeping our understanding current, we rely on these publications to help educate our students. How we use primary literature in biotechnology education Unlike the faculty in research universities, many of the instructors in community college biotech programs are scientists with backgrounds in the biotech industry. These instructors routinely assign scientific papers as part of their courses since they are training biotechnology technicians and industry technicians are expected to be able to read this type of literature. Industry advisory boards also encourage the use of primary literature. At Austin Community College (Texas), students use research articles to design and write experimental protocols. At Shoreline Community College (Washington), students in the Molecular Biology course give presentations on research papers. I also refer students to the primary literature in my bioinformatics courses. And I draw extensively on primary literature when I design instructional materials and learning activities. Our educational practices will be severely impacted by restricting access to the literature. If we're required to purchase individual articles, often priced at $30 each, we will either have to end these practices or consider becoming Internet pirates sailing on the good ship Napster.pdf. Some of my experiences with the problems of accessing primary literature Twenty years ago, as a new college instructor, I was thrilled when PubMed became free and my students could start reading abstracts on-line. I still spent hours photocopying and organizing papers for student presentations and research projects but having access to abstracts was a great beginning. Not only did I want students to learn how to scientific papers, I wanted them to understand the difference between the primary literature and the articles you might read in the newspaper or popular magazines like Discover or Wired. I wanted students to see for themselves how some details might get left out, how the same details could be presented in different ways and multiple groups might arrive at different conclusions. My instructor colleagues and I were especially happy when NIH began to require that NIH-funded research be open to the public. Now, we could get papers ourselves and we could start requiring our students to read papers, too. Even some of the high school teachers I know started asking students to use PubMed and skim papers on topics like genetic disease. Doing the hard thing isn't always easy In the days when research papers were pay per view, many of us shied away from assigning primary research. After all, it's not realistic to expect students to spend $30 to[...]

Genomic funding goes Mendelian

Tue, 06 Dec 2011 15:39:31 -0500

In simple Mendelian genetics, a single change in one gene can produce a large change in mortality. The National Human Genome Research Institute (NHGRI) will be funding genomics studies on Mendelian traits using a similar strategy.

NHGRI will fund a small number of centers, dominant centers you might say, and look for large changes. The sequencing centers that will benefit are the Broad Institute, Washington University, and Baylor College of Medicine. For the next four years, the big three will be dividing $86 million a year according to a press release from NHGRI. I'm not sure what algorithms predict a larger return from funding a smaller number of researchers, but the future looks like fun for those on a small budgets who can figure out how to slurp up the data and quickly spit out results.

Studies on Mendelian disorders will benefit from the proposed funding plan as well. According to the NIH press release, only half of the estimated 6,000 rare diseases, inherited in a Mendelian pattern, have been linked to a genetic cause. Although each disease is rare, in combination, these diseases affect approximately 25 million Americans. Today's DNA sequencing technologies offer an unprecedented ability to find the basis for these diseases, particularly when the genomes of entire families are compared.

Which brings us to clinical sequencing and new interesting issues.

Earlier genetic tests raised all kinds of ethical controversies. Does everyone have a right to be tested? Should test results be shared with one's family? Should parents be allowed to test children? Should someone have a right to know, to not know, etc. Identifying all the stakeholders and their issues can make your head spin.

And those tests typically looked at single genes.

Today, when we sequence a genome, we will find much more information about many thousands more genes whether we want it or not. Genome sequencing is like remodeling. A simple quest to check out a foundation always goes along with the chance of finding water leaks or ant colonies.

We could sequence a genome from a cancer patient for example, to determine the best drug for treatment, and uncover an undiagnosed predisposition to some other bad news of kind of trait. What doctor wants to share the news that they can cure someone's cancer but that early Alzheimer's gene they found, uh sorry, maybe you want to look into assisted living?

Many of us see enormous potential in genomic sequencing. But, in the end successfully using genomics will require us to go well beyond the work of developing the technology to prepare genome sequencing for the clinic. We're going to have to prepare the clinic for genome sequencing.

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Biotechnology Education - what's happening folks?

Mon, 28 Nov 2011 23:12:32 -0500

Like everything else, if we want to know what's going on, we have to ask.

So, it's time once again for the 2011-2012 National Biotechnology/Life Sciences Program Survey.

Yes, indeed.

Federal and state agencies will use the results to determine how best to support programs like yours. This study will also help prospective students and industry employers find your program. Survey results will be available to you to help with program planning, grant activities, and more.

We only want one person from each biotechnology / biomanufacturing / bioscience program to complete the survey. If you are not the right person to complete the survey, please get your college's biotechnology/life sciences program administrator to spare 15 minutes and fill this out.

We think the survey will take 15 minutes or less to complete.

Your participation is crucial to ensuring that the results accurately represent this important industry. Whether or not your college currently offers a biotechnology/life sciences program, your input is essential. The survey includes programs that are in the planning stages, as well as ways that colleges incorporate these subjects into other courses.

The survey asks about:
· Program characteristics,
· Student demographics, and
· Degrees and certificates awarded.

To start the survey, please click on the link below.

https://www.surveymonkey.com/s/BioLinkNationalSurvey

This survey is being conducted by Bio-Link's Independent Evaluator, the Social and Economic Sciences Research Center at Washington State University (WSU-SESRC). To request a paper version of the survey or to complete the survey via telephone, please contact Candiya Mann, Project Director, at candiya@wsu.edu

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Community colleges and the bioeconomy: it's time to step up and share

Fri, 25 Nov 2011 14:37:43 -0500

What roles should community colleges play in training the bioeconomy workforce of the future?

Send your answers to bioeconomy@ostp.gov by Dec. 6th.

One night towards the end of October, we happened to meet with someone who could tell us more.

We asked him about a request for information (RFI) soliciting input on the bioeconomy, that some of us saw posted on the Federal Register web site.

"What could information could we provide?," We asked (a little skeptically).

"Does the Whitehouse really want our input on ways to stimulate the bioeconomy and build the bioscience workforce?"

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Genomes with benefits

Sun, 02 Oct 2011 17:56:01 -0500

For the past few days I've been avidly following Daniel MacArthur's tweets from the Personal Genome Conference at Cold Spring Harbor(@dgmacarthur #cshlpg).

The Personal Genomics tweets aren't just interesting because of the science, they're interesting because MacArthur and others have started to take on the conventional dogma in genetic ethics.

For years, there has been a strong message from the clinical genetics and genetics education community that genetic information is dangerous.

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"It's all about Aunt Millie"

Fri, 06 May 2011 15:23:57 -0500

"It's all about saving Aunt Millie"
Bob Swanson
Co-Founder of Genentech

I just learned today that Jim DeKloe, who wrote this post as a guest author a few years ago is giving a webinar on May 11th on protein purification from industrial enzymes to cancer therapy.

Jim's webinar, offered through Bio-Rad, has two sessions at 3 pm Eastern and 7 pm Eastern. Registration is free and you can register HERE.

Jim is one of the most inspirational educators I know and he's the sort of person that reminds you why educating students about biotechnology careers is important. His moving story is one that always reminds me that there's more to biotechnology than just the science.

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NSF Funding opportunities for Two Year Colleges

Fri, 06 May 2011 12:36:55 -0500

The National Science Foundation recently announced an ambitious plan to transform biology education across the United States called "Vision and Change." Funding for this mission is being provided by a new NSF grant program called "TUES" for Transforming Undergraduate Education in Science.

(image) This finding may have been a surprise to some, but two year colleges have a disproportionate impact on biology education in the U.S. (1, 2). At least half of the country's biology students are enrolled at two year colleges. Additionally, community colleges often provide the only college-level biology courses for the nation's high school biology teachers. Community college biotechnology programs, in particular, are also leading providers of professional development opportunities for high school instructors.

One of the challenges, however, in transforming a practice as extensive as college biology teaching is building cohorts and getting seed money out to the people who can implement this change. This is even more difficult with two-year college faculty because community colleges and community college faculty lack the grant-writing experience and support found at the R1 universities. Their goal is to educate students, not bring in grant funds.

The NSF is working to help community college faculty learn how to write grants and get more funds to make transforming biology education go beyond an appealing vision.

If you are a faculty member at a two year college, the NSF is sponsoring a workshop from July 19-22nd in Reno, NV and will provide up to $750 to help with travel expenses and lodging.

Apply here.

References:
1. Vision and Change in Undergraduate Biology Education, A Call to Action. 2011. www.visionandchange.org

2. Fletcher LA, & Carter VC (2010). The important role of community colleges in undergraduate biology education. CBE life sciences education, 9 (4), 382-3 PMID: 21123677

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Funding dreams and writing Advanced Technology Education proposals for the National Science Foundation

Mon, 02 May 2011 12:53:25 -0500

It only takes a quick trip to the grocery store to see that familiar jobs are vanishing. Unless you're in Oregon, grocery store checkers are going the way of gas station attendants, travel agents, and secretaries. Jobs are changing, new jobs require different skills, and even those jobs will be obsolete within a short time.

Community colleges can cushion the blow by developing education programs in response to the needs of their local communities.

Not only do these programs help displaced workers, they help their communities attract new businesses and support economic growth. Georgia's Technical College System, for example, was credited with helping to convince Dendreon to locate a new $70 million biomanufacturing plant, with 550 jobs and an annual combined payroll close to $35 million in an Atlanta suburb (1).

But, where do schools get the seed money to start new programs in the first place? Surprisingly, one of the best sources of start up funds is the National Science Foundation's program in Advanced Technology Education (ATE) (2). The NSF:

"anticipates that approximately $64.0 million will be available for new and continuing awards in this program in FY2012. Funding in all years is subject to the availability of funds. The program expects to make 75-90 new awards per year."

The impact from the ATE program is huge. In 2009, the ATE program supported programs at 1300 education institutions and served 85,300 students, and 58,100 educators (3).

If you're interested in applying for funds, ATE grant proposals are due in October. The time to start writing is now.

If you want to learn how to develop a plan and write a proposal, Bio-Link is offering a free webinar on May 24th. (The original data was the 17th but we had to change it.). Dr. Linnea Fletcher, a former NSF program officer, and a Bio-Link Co-PI, will be presenting.

cross-posted at: Bio-Link.org

References:
1. Alex Philippidis, 2009. Airport Site, Georgia Tax Credit Entices Dendreon to Base New Biomanufacturing Plant in State. Genomeweb BioRegion News.
2. Advanced Technological Education (ATE) Program Solicitation 2011
3. Evaluate Advanced Technological Education Survey 2010 Fact Sheet

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Did 12 year olds make my iPhone?

Sun, 01 May 2011 10:26:21 -0500

Last night we went to see "The Agony and the Ecstasy of Steve Jobs" by Mike Daisey. Two hours vanished as we sat riveted and listened to interspersed stories of Apple and Shenzhen. Mike spoke of Apple and computers as a lover, familiar with the details, and knowledgeable in the special language of geeks and engineers. He was hysterically funny.

And we all understood.

After all, the night at the play was organized as a spring celebration by the Washington Technology Industry Association, a group intimately familiar with the ways of tech.

From the music preceeding the show, to Mike's stories of dabbling with the "heretical Linux" platform and even sleeping around with Windows, now and then in the late 90's, we laughed, having been there ourselves and lived those moments.

But once place we had never been was Shenzhen, China. We never knew that 50% of our electronics were made by Foxconn, a company of over 400,000 people who work in buildings surrounded by nets designed to catch suicidal workers. We never knew that teenagers worked 32 hour shifts and sometimes died afterwards. We never knew that our lovely Iphones and Ipads were assembled by hand, in 12 hour shifts, in silence, because people in China are cheaper than machines.

And we certainly didn't know the workers were children.

Mike described talking to people outside of factories, touring the plants, and hearing people's stories. And we found ourselves "infected with the mind virus" just as he described, knowing more than we wanted.

Perhaps he unfairly picked on Apple. It seems likely that Androids, Blackberrys, and other high tech items are built the same way. We expect computers that pride themselves on being cheap to be built in shoddy, unseemly surroundings.

But we hold Apple to a higher standard. Mike posed the question, as a long-time fan of Apple products and committed Apple user. He asked how Apple, a company so obsessed with detail, be unaware that their products are being assembled by children, in dystopian 1984 style factories.

We went home after the play and turned on our computers. And thought maybe there should be the computer equivalent of fair-trade coffee.

Maybe the Gates Foundation could detour a bit from malaria and push computer factories to "think different."

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Strategic plans and genome sequencing

Mon, 14 Feb 2011 15:36:50 -0500

This morning I attended a "bloggers-only" conference call with Dr. Eric Green and the folks from the NIH Human Genome Research Institute (NHGRI) to hear about NHGRI's new strategic plan. The new plan represents a shift away from viewing the genome through a lens marked "for research use only" and towards the goal of making the genome useful as a clinical tool. As a consequence, we will see a greater emphasis on funding activities that support clinical work. For example, it's not always clear how variations in the genome are related to disease. NHGRI might fund projects that help sort and categorize this information. It's certainly not clear yet what NHGRI should do to help patients and physicians handle the genetic information onslaught, particularly in the area of personal genomics. Personally, I think some of the folks at NHGRI might find it eye-opening if they were to sign up with 23andme and see the sorts of genetic information the general public can get. My family and I all took advantage of the "genetic testing special" last December and mailed 23andme our tubes of spit. Since we got the results, we've had lots of fun figuring out who inherited which alleles from who and learning why some of us can drink coffee at night. We've also spent some time explaining to our kids that some of results are far less meaningful than others and why a 1.1 fold increase in risk for some disorder is not terribly alarming. I have to admit, 23andme has some pretty nice videos and education resources.  Getting teenagers to sort through all the information is not easy, but the information is there, if they care to look.Which brings me to the point where I found the conference call a bit disappointing. In the phone call, Dr. Green called out education and training as one of the important cross-cutting themes that must be supported if the benefits of genomics are going to be wide-spread. Genomic information isn't likely to be used widely unless the general public understands those benefits. Since NHGRI doesn't fund many education programs, except at a graduate level, and since the one NIH institute that does fund education (NCRR) is being dismantled, I was interested to know if NHGRI has any plans to take over that role. So, I asked Dr. Green if NHGRI has any specific plans to support genomics education. His answer was longer. The short version was "no." At this point, I really don't know why there's a special box in the strategic report on education and training. Maybe those subjects are only mentioned because we know they're important, not because we plan to do anything. Maybe, like personal genomics, we'll just leave that subject to groups like 23andme. Reference Green ED, Guyer MS, National Human Genome Research Institute, Overall leadership, Green ED, Guyer MS, Coordination of writing contributions (see Acknowledgements for list of other contributors), Manolio TA, & Peterson JL (2011). Charting a course for genomic medicine from base pairs to bedside. Nature, 470 (7333), 204-13 PMID: 21307933 Read the comments on this post...[...]

The origin of creationism

Wed, 09 Feb 2011 15:24:27 -0500

Have you ever wondered if creationism was intelligently designed? Most of my colleagues tend to dismiss creationism as generally nutty and not worth bothering about. But, every now and then, we did get the odd situation with a few students who disagree or state legislatures that get a little confused about the definition of science. This video lecture is a bit long, but definitely interesting. title="YouTube video player" width="450" height="283" src="http://www.youtube.com/embed/XpNvA8NX4Bg" frameborder="0" allowfullscreen> Read the comments on this post...(image)

Mining the job search sites for life science positions

Mon, 07 Feb 2011 11:18:32 -0500

Disclaimers - just so you know...This information is cross-posted at www.bio-link.orgAll the data and graphs in this post were obtained from Simplyhired.com.  I do not have any kind of commercial affiliation with this company I found their site via GenomeWeb.Having worked around biotechnology for several years, I thought I was pretty familiar with biotech job descriptions. I decided to test this assumption by playing with the data at SimplyHired.com.Being able to quickly search with different terms and examine trends in job postings has proved to be an enlightening experience. These kinds of searches would be really useful for anyone who is conducting a job search or considering what courses to study for a future career. What terms are used to describe biotech and life-science jobs? It's important to realize that  when we search biotech and life science job data, we get different  results when we use different search terms, even if the positions are roughly equivalent. Not only is this insight important for looking at data, it's important for using the right terms when we look for work.SimplyHired.com uses an algorithm that searches for the presence of a term in a job description. All job descriptions that contain a term are counted and displayed. Although we can get more results for more generic terms, our resulting numbers are too high and contain too little detail. For example, searching with the word "Biology" gives us adds for biology instructors, scientists, tutors, internships, and industry positions, among others. In the graph below, we see that the numbers for "Biological Science Technician" dwarf the numbers of available positions for biomanufacturing, biotechnicians, and biology technicians.    "Biological Science Technician", Biomanufacturing, Biotechnician, "Biology Technician" trends "Biological Science Technician" jobs | Biomanufacturing jobs | Biotechnician jobs | "Biology Technician" jobs     ** If you click the links below any of the graphs, you can see the data too. Read the rest of this post... | Read the comments on this post...[...]

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