Tag Archives: science

Heroes of CRISPR Through Twitter’s Eyes: A Sequence

Who knows? Perhaps the story behind the story began here, last October, with a tweet about an article in Wired on “The Heroes of CRISPR.”

Zhang, Sarah. The Battle Over Genome Editing Gets Science All Wrong. WIRED Magazine 10.04.15. http://www.wired.com/2015/10/battle-genome-editing-gets-science-wrong/

Maybe that made someone else think that there really ought to be an article with that title. Although, hints of this arose earlier, with articles like “Who Owns CRISPR?” from last April and “Law, history and lessons in the CRISPR patent conflict” from March, or even the 2014 article “First CRISPR-Cas patent opens race to stake out intellectual property“. In any case, the “Heroes of CRISPR” debate which erupted on Twitter (reaching trending status yesterday) has roots far deeper than the article of the same name, which triggered the flood, or even the US Patent Office’s recent insertion into the CRISPR patent battle.

Zhang, Sarah. An Arcane Patent Law May Decide Crispr’s Big Legal Fight. WIRED Science 01.05.16. http://www.wired.com/2016/01/crispr-patent-dispute-gets-really-arcane/

The early tweets were mostly supportive, creating awareness of what is genuinely an eloquent and educational article, especially for those outside the field. There were, however, hints of the later discord even among the earliest tweets. Later concerns arose more from informed readers on the inside of the professions working with CRISPR and aware of the personalities and politics behind the piece, and then snowballed.

* Early Tweets about ‘Heroes of CRISPR’
* The Heat rises
* The Response(s)
* Ongoing debate
* More information

EARLY TWEETS ABOUT ‘HEROES OF CRISPR’

12:48 PM – 14 Jan 2016

1:17 PM – 14 Jan 2016

1:33 PM – 14 Jan 2016

1:47 PM – 14 Jan 2016

2:09 PM – 14 Jan 2016

3:52 PM – 14 Jan 2016

4:01 PM – 14 Jan 2016

4:50 PM – 14 Jan 2016

5:52 PM – 14 Jan 2016

6:22 PM – 14 Jan 2016

6:38 PM – 14 Jan 2016

6:44 PM – 14 Jan 2016

7:26 PM – 14 Jan 2016

8:22 PM – 14 Jan 2016

1:35 AM – 15 Jan 2016

3:17 AM – 15 Jan 2016

7:02 AM – 15 Jan 2016

7:35 AM – 15 Jan 2016

8:11 AM – 15 Jan 2016

9:04 AM – 15 Jan 2016

9:10 AM – 15 Jan 2016

12:26 PM – 15 Jan 2016

THE HEAT RISES

10:31 AM – 15 Jan 2016

10:36 AM – 15 Jan 2016

10:49 AM – 15 Jan 2016

11:18 AM – 15 Jan 2016

12:41 PM – 15 Jan 2016


We Can Now Edit Our DNA. But Let’s Do it Wisely | Jennifer Doudna | TED Talks https://www.youtube.com/watch?v=TdBAHexVYzc

6:55 PM – 15 Jan 2016

THE RESPONSE(S)

4:01 PM – 16 Jan 2016

4:03 PM – 16 Jan 2016

4:11 PM – 16 Jan 2016

4:14 PM – 16 Jan 2016

4:21 PM – 16 Jan 2016

4:24 PM – 16 Jan 2016

5:44 PM – 16 Jan 2016

4:12 PM – 17 Jan 2016

5:51 AM – 17 Jan 2016

PubPeer on Heroes of CRISPR

11:43 AM – 19 Jan 2016

11:57 AM – 19 Jan 2016

1:19 PM – 19 Jan 2016

ONGOING DEBATE

3:19 PM – 18 Jan 2016

7:04 PM – 18 Jan 2016

3:33 PM – 19 Jan 2016

3:48 PM – 19 Jan 2016

3:54 PM – 19 Jan 2016

4:11 PM – 19 Jan 2016

5:06 PM – 19 Jan 2016

5:24 PM – 19 Jan 2016

5:30 PM – 19 Jan 2016

6:56 PM – 19 Jan 2016

6:58 PM – 19 Jan 2016

7:08 PM – 19 Jan 2016

7:45 PM – 19 Jan 2016

7:46 PM – 19 Jan 2016

7:52 PM – 19 Jan 2016

"Heroes of CRISPR" commentary

9:56 AM – 20 Jan 2016

MORE INFORMATION

USPTO: CRISPR Patents: http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO2&Sect2=HITOFF&p=1&u=%2Fnetahtml%2FPTO%2Fsearch-bool.html&r=0&f=S&l=50&TERM1=crispr&FIELD1=&co1=AND&TERM2=&FIELD2=&d=PTXT

March 6, 2014. Doudna Patent, Methods and compositions for rna-directed target dna modification and for rna-directed modulation of transcription (US 20140068797 A1). http://www.google.com/patents/US20140068797

Apr 15, 2014: Zhang Patent, CRISPR-Cas systems and methods for altering expression of gene products (US 8697359 B1) http://www.google.com/patents/US8697359 | http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO2&Sect2=HITOFF&p=1&u=%2Fnetahtml%2FPTO%2Fsearch-bool.html&r=1&f=G&l=50&co1=AND&d=PTXT&s1=8,697,359.PN.&OS=PN/8,697,359&RS=PN/8,697,359

July 11, 2015: CRISPR – Will This Be the Last Great US Patent Interference? http://blog.patentology.com.au/2015/07/crispr-will-this-be-last-great-us.html

November 9, 2015: The Crispr Quandary:  A new gene-editing tool might create an ethical morass — or it might make revising nature seem natural. http://www.nytimes.com/2015/11/15/magazine/the-crispr-quandary.html?_r=0

December 29, 2015: The CRISPR Patent Interference Showdown Is On: How Did We Get Here and What Comes Next? https://law.stanford.edu/2015/12/29/the-crispr-patent-interference-showdown-is-on-how-did-we-get-here-and-what-comes-next/

January 8, 2016: DuPont in CRISPR-Cas patent land grab http://www.nature.com/nbt/journal/v34/n1/full/nbt0116-13.html

January 12, 2016: For journalists: Statement and background on the CRISPR patent interference process https://www.broadinstitute.org/what-broad/areas-focus/project-spotlight/journalists-background-patent-process

January 12, 2016: USPTO Declares Interference Proceeding to Adjudicate CRISPR Patent Spat https://www.genomeweb.com/business-news/uspto-declares-interference-proceeding-adjudicate-crispr-patent-spat

January 12, 2016: Bitter fight over CRISPR patent heats up http://www.nature.com/news/bitter-fight-over-crispr-patent-heats-up-1.17961

January 13, 2016: USPTO ignites CRISPR/Cas9 patent battle http://www.lifesciencesipreview.com/news/uspto-ignites-crispr-cas9-patent-battle-1280

January 13, 2016: Control of CRISPR, biotech’s most promising breakthrough, is in dispute https://www.washingtonpost.com/news/wonk/wp/2016/01/13/control-of-crispr-biotechs-most-promising-breakthrough-is-up-for-grabs/

January 15, 2016: CRISPR Patent War: Billions at Stake for UC Berkeley http://ww2.kqed.org/futureofyou/2016/01/15/crispr-patent-war-billions-at-stake-for-uc-berkeley/

January 16, 2016: A Brief History Of The Gene-Editing Tool That Is Changing Science, Scientists have now actually watched the DNA-editing tool in action http://www.vocativ.com/news/263157/crispr-cas9/

January 19, 2016: Controversial CRISPR history sets off an online firestorm http://www.statnews.com/2016/01/19/crispr-history-firestorm/

January 20, 2016: A social media war just erupted over the biotech innovation of the century https://www.washingtonpost.com/news/wonk/wp/2016/01/20/is-a-history-of-biotechs-hottest-breakthrough-propaganda/

Celebrating Women Inventors at UofM (for #AdaLovelaceDay)

Ada Lovelace Day in Second Life

Why Ada Lovelace Day matters, asks the Guardian today. Usually people celebrate by highlighting famous women scientists. I asked myself, what about right here, right now? What are women scientists and inventors doing at the University of Michigan?

I figured the best way to find out was to go through the UM Tech Transfer database of Available Technologies for licensing. I skimmed the most recently deposited 100 inventions, looking for women. I found inventions in education and healthcare (even new cell lines!). I also found women inventing new batteries and biosensors, researchers working in engineering and code and physics, and even, yes, gamma rays! Some were prolific with MANY inventions listed recently. Most had one or two. They are ALL fabulous. And I am proud to say I know some of them personally. Take a look. See what cool smart women are inventing here. And remember: The sky is the limit!

Elizabeth W. Anderson – Responsible Conduct of Research for K Awardees (RCR4K) | Trainer’s Guide for Responsible Conduct of Research for K Awardees (RCR4K)

Valeria Bertacco – Post-Silicon Bug Diagnosis with Inconsistent Executions

Sarah Hawley – iCanDecide Conjoint Analysis Breast Cancer Treatment Decision Aid (ICanDecide)

Jane E. Huggins – Direct Brain-Computer Interface for Cognitive Assessment

Lori L. Isom – beta1/Contactin Cell Line

Helen C. Kales – WeCareAdvisor (based on her DICE method for dementia management)

Naheed Wali Khan – Multimodal Imaging in Retinal Diseases

Michelle Meade – Mobile Game for Spinal Cord Injury Health and Behavioral Rehabilitation

Sandra I. Merkel – Face, Legs, Activity, Cry, Consolability (FLACC) Observational Tool as a Measure of Pain

Janis Miller – Self-Instructional Voiding/Intake Diary and Individualizing Target Bladder Health Goals through Beverage Management

Mahta Moghaddam –
Method of Including Full-Wave Source Model in Acoustic and Electromagnetic Scattering and Inverse Scattering Formulations
Antenna and Propagation Model for Free-space Measurements and Experimental Inverse Scattering
Method for Large-Domain Microwave Breast Imaging

Sara Pozzi – Combined Scintillator-based Neutron and Gamma-ray Dosimeter

Emily Kaplan Mower Provost – Smartphone app for aphasia therapy

Mary C. Ruffolo PhD – Online evidence-based practice training modules

Melanie S. Sanford –
Organic Anolyte Materials for Flow Batteries
Generation of Ag18F and its use in the synthesis of PET radiotracers

Mary Simoni – Block M Records (University of Michigan Recordings) (Catalog)

Nancy Butler Songer – Evidence-based Learning Method for K-12 Students to Evaluate the Ecological Impacts of Climate Change

Laurie Sutch – Teaching and Technology Collaborative Workshop Registration System

Amy J. Teddy – Online concussion education for parents and coaches

Margaret S. Wooldridge – Cylinder Pressure and Heat Release Analysis Tool for Advanced Combustion Engines

Laboratory Life Online, Part 1 (A HOTW Post)

Second Life: Nanotechnology Island

There has been a lot of science communication (#SciComm) action on Twitter recently centering around what does life look like for real scientists. I have a head start on this because when I was a little tyke, my dad dragged me into the lab with him and told me things like to watch the door of the High Wind Velocity Testing Lab so that the tornado didn’t get out while he was working on his mass spectrometer lithium sample testing. What can I say? I was gullible. So all those fun lifestyle pithy tweets will come in a later post, but for today, here is proof of presence of laboratories on Twitter. For the record, there are a lot more of these in each category, because Twitter’s search limits don’t return complete results for matches to the search criteria. Basically, that means I found a lot of these by browsing, when I should have been able to find them through search. I hope this is a useful resource. Enjoy!

ABOUT LABORATORIES

American Laboratory https://twitter.com/AmericanLab
Lab Design News https://twitter.com/labdesignnews
Lab Guru https://twitter.com/Labguru
Lab Life (@LabLife) https://twitter.com/LabLife
Lab Spaces https://twitter.com/LabSpaces
Lab TV https://twitter.com/LabTVCuriosity
Laboratory EQAS https://twitter.com/LaboratoryEQAS
Laboratory Equipment https://twitter.com/LabEquipment
Laboratory News https://twitter.com/laboratorynews
Laboratory Products https://twitter.com/labproductsnews

MICHIGAN LABS

Cardinale Lab (ecology and biodiversity lab) https://twitter.com/CardinaleLab
Decision Lab https://twitter.com/DecisionLab
Edelstein Lab https://twitter.com/EdelsteinLab
Lauring Lab https://twitter.com/LauringLab
Mahon Lab @CMU_Antarctica https://www.twitter.com/CMU_Antarctica
MiNDLab https://www.twitter.com/MiNDLab_umich
Michigan Tech High Performance Computing (HPC) @MichiganTechHPC https://twitter.com/MichiganTechHPC
MLabs (pathology) https://www.twitter.com/MLabsUM
National Superconducting Cyclotron Laboratory (@NSCL) https://twitter.com/NSCL
NOAA Great Lakes Environmental Research Lab (GLERL) https://twitter.com/NOAA_GLERL
Tronson Lab https://twitter.com/tronsonlab
U.M. Sex Lab https://twitter.com/SexualityLab
U Mich Concept Lab https://twitter.com/UMichConceptLab
University of Michigan Childhood Disparities Research Laboratory (@UMCDRL) https://twitter.com/UMCDRL

U.S. NATIONAL LABS

Ames Laboratory @Ames_Laboratory https://twitter.com/Ames_Laboratory
Argonne National Lab @argonne https://twitter.com/argonne
Berkeley Lab @BerkeleyLab https://twitter.com/berkeleylab
Berkeley Lab CS @LBNLcs https://twitter.com/LBNLcs
Brookhaven Nat’l Lab @BrookhavenLab https://twitter.com/brookhavenlab
DOE Science https://twitter.com/doescience
Energy Sciences Network (ESnet) @ESnetUpdates
Federal Laboratory Consortium for Technology Transfer (FLC) @federallabs
Fermilab @Fermilab
Idaho National Lab @INL https://twitter.com/INL
ISS U.S. National Laboratory, Center for the Advancement of Science in Space (CASIS) (@ISS_CASIS) https://twitter.com/iss_casis
Jefferson Lab P.A. @Jblab
LBNL Media Report @LBNLmediareport
Lawrence Livermore National Laboratory (LLNL) @Livermore_Lab https://twitter.com/Livermore_Lab
Los Alamos National Lab (LANL) @LosAlamosNatLab https://twitter.com/LosAlamosNatLab
Los Alamos National Laboratory (LANL) – Health (@LANL_Health) https://twitter.com/lanl_health
Los Alamos National Laboratory (LANL) – Space https://twitter.com/lanl_space
National Energy Research Scientific Computing Center (NERSC) https://twitter.com/NERSC
National Energy Technology Laboratory (NETL) @NETL_News https://twitter.com/NETL_News
National High Magnetic Field Laboratory @NationalMagLab https://twitter.com/nationalmaglab
National Nuclear Security Administration (NNSA) https://twitter.com/NNSANews
National Renewable Energy Laboratory (NREL) @NREL
NASA Jet Propulsion Laboratory (JPL) @NASAJPL https://twitter.com/NASAJPL
NOAA Atlantic Oceanographic & Meteorological Laboratory (AOML) https://twitter.com/noaa_aoml
NOAA Great Lakes Environmental Research Lab (GLERL) https://twitter.com/NOAA_GLERL
Oak Ridge National Laboratory @ORNL https://twitter.com/ORNL
Oak Ridge National Lab, Manufacturing Demonstration Facility (ORNL Manufacturing) @ORNLMDF https://twitter.com/ORNLMDF
Pacific Northwest National Laboratory (PNNL) @PNNLab https://twitter.com/pnnlab
Princeton Plasma Physics Laboratory (PPPL) @PPPLab
Sandia National Labs @SandiaLabs https://twitter.com/SandiaLabs [Sandia National Labs @SandiaLabsUVM https://twitter.com/SandiaLabsUVM%5D
Sanford Lab @SanfordLab https://twitter.com/SanfordLab
Savannah River National Laboratory @SRSNews https://twitter.com/SRSNews
SLAC National Accelerator Laboratory @SLAClab https://twitter.com/SLAClab
U.S. Army Research Labs https://twitter.com/ArmyResearchLab
U.S. Global Development Lab https://twitter.com/GlobalDevLab

MORE LABS WORTH KNOWING

Arne Lindqvist Lab (cancer research) @LindqvistLab https://twitter.com/LindqvistLab
Boulby Laboratory (deep underground science) https://twitter.com/BoulbyLab
Cavendish Laboratory (physics) https://twitter.com/DeptofPhysics
Happe Lab (autism research) https://twitter.com/HappeLab
Hewlett Packard Labs https://twitter.com/hplabs
HHS Idea Lab https://twitter.com/HHSIDEALab
MIT Lincoln Laboratory https://twitter.com/MITLL
MIT Media Lab https://twitter.com/medialab
National Archives & Records Administration (NARA) Media Labs https://twitter.com/NARAMediaLabs
Public Laboratory (open source) @PublicLab https://twitter.com/PublicLab
Suicidal Behaviour Research Laboratory @SuicideResearch https://twitter.com/suicideresearch
The Food Lab https://twitter.com/TheFoodLab
U.K. National Nuclear Laboratory @UKNNL https://twitter.com/uknnl
Wired Gadget Lab @GadgetLab https://twitter.com/gadgetlab
Wise Laboratory (toxicology) https://twitter.com/WiseLaboratory

From the Arxiv (What Caught My Eye Last Week)

Quantifying the impact of weak, strong, and super ties in scientific careers
Alexander Michael Petersen
PDF: http://arxiv.org/pdf/1509.01804v1.pdf
Soundbite: “We find that super ties contribute to above-average productivity and a 17% citation increase per publication, thus identifying these partnerships – the analog of life partners – as a major factor in science career development.”

Do we need another coffee house? The amenity space and the evolution of neighborhoods
César A. Hidalgo, Elisa E. Castañer
PDF: http://arxiv.org/pdf/1509.02868v1.pdf
Soundbite: “Neighborhoods populated by amenities, such as restaurants, cafes, and libraries, are considered to be a key property of desirable cities. … Finally, we use the Amenity Space to build a recommender system that identifies the amenities that are missing in a neighborhood given its current pattern of specialization.”

Liberating language research from dogmas of the 20th century
Ramon Ferrer-i-Cancho, Carlos Gómez-Rodríguez
PDF: http://arxiv.org/pdf/1509.03295v1.pdf
Soundbite: ” Those tenets can be summarized as a belief in the existence of word order constraints that cannot be explained by evolutionary processes or requirements of performance or learning, and instead require either (a) heavy assumptions that compromise the parsimony of linguistic theory as a whole or (b) explanations based on internal constraints of obscure nature.”
Interesting: “We submitted our commentary to PNAS but it was rejected. We hope that the availability of our submission helps to liberate language research from dogmas of the 20th century”

Estimating Reproducibility in Genome-Wide Association Studies
Wei Jiang, Jing-Hao Xue, Weichuan Yu
PDF: http://arxiv.org/pdf/1508.06715v1.pdf
Soundbite: “This can be used to generate a list of potentially true associations in the irreproducible findings for further scrutiny.”

Nucleosome positioning: resources and tools online
Vladimir B. Teif
PDF: http://arxiv.org/pdf/1508.06916v4.pdf
About: Gene Regulation Info
Includes: Nucleosome positioning datasets sorted by cell type

Combining exome and gene expression datasets in one graphical model of disease to empower the discovery of disease mechanisms
Aziz M. Mezlini, Fabio Fuligni, Adam Shlien, Anna Goldenberg
PDF: http://arxiv.org/pdf/1508.07527v1.pdf
Soundbite: “It is not unusual to observe a significant gene expression change in thousands of genes, the majority being a downstream, rather than the driver, effect (e.g. inflammation, drug response, etc) Additionally, and more importantly, there is a large heterogeneity in gene expression in cancer: many patients within the same subtype will appear to have an abberant expression. These variations are of unknown cause.”

Using Genetic Distance to Infer the Accuracy of Genomic Prediction
Marco Scutari, Ian Mackay, David Balding
PDF: http://arxiv.org/pdf/1509.00415v2.pdf
Soundbite: ” In human genetics, decay curves could be used study to what extent predictions are accurate and thus to improve the performance of medical diagnostics for the general population. In plant and animal breeding, on the other hand, it is common to incorporate distantly related individuals in selection programs to maintain a sufficient level of genetic variability.”

Population genomics of intrapatient HIV-1 evolution
Fabio Zanini, Johanna Brodin, Lina Thebo, Christa Lanz, Göran Bratt, Jan Albert, Richard A. Neher
PDF: http://arxiv.org/pdf/1509.02483v1.pdf
Soundbite: “In most patients, the virus populations was initially homogeneous and diversified over the years, as expected for an infection with a single or small number of similar founder viruses (Keele et al., 2008). In two patients, p3 and p10, the first sample displayed diversity consistent with the transmission of several variants from the same donor.”
Soundbite: “Our reasoning proceeds as follows. Figure 6B indicates that diversity accumulates over a time frame of 2-4 years, i.e., about 1,000 days. Recombination at a rate of 10−5/bp/day hits a genome on average every 100 bps in 1000 days. Mutations further apart than 100bps are hence often separated by recombination and retain little linkage consistent with the observed decay length in Figure 7.”

Inadequate experimental methods and erroneous epilepsy diagnostic criteria result in confounding acquired focal epilepsy with genetic absence epilepsy
Raimondo D’Ambrosio, Clifford L. Eastman, John W. Miller
PDF: http://arxiv.org/pdf/1509.01206v1.pdf
Soundbite: “Because the authors could not induce focal seizures by FPI, they ended up comparing absence epilepsy in their controls with absence epilepsy in FPI rats, and concluded that they look similar. They also used inappropriate epilepsy diagnostic criteria that cannot distinguish between focal non-convulsive seizures and genetic absence epilepsy. Moreover, the authors failed to consider all literature conflicting with their conclusion, and surmised similarities between the absence epilepsy in their rats with the focal seizures we induce by rpFPI.”

Reduction of Alzheimer’s disease beta-amyloid pathology in the absence of gut microbiota
T. Harach, N. Marungruang, N. Dutilleul, V. Cheatham, K. D. Mc Coy, J. J. Neher, M. Jucker, F. Fåk, T., Lasser, T. Bolmont
PDF: http://arxiv.org/pdf/1509.02273v1.pdf
Soundbite: “Our results indicate a microbial involvement in the development of Alzheimer’s disease pathology, and suggest that microbiota may contribute to the development of neurodegenerative diseases.”

Fractal Fluctuations in Human Walking: Comparison of Auditory and Visually Guided Stepping
Philippe Terrier
PDF: http://arxiv.org/pdf/1509.01913v1.pdf
Soundbite: “[B]ecause it can be assumed that AC and VC mobilize the same motor pathways, they can probably be used alternatively in gait rehabilitation. The efficiency of VC to enhance walking abilities in patients with neurological gait disorders needs further studies. However, the high gait variability induced by VC might have detrimental effects, for instance, a lower dynamic balance. This should be taken into account in the development of VC rehabilitation methods.”

The Brain Uses Reliability of Stimulus Information when Making Perceptual Decisions
Sebastian Bitzer, Stefan J. Kiebel
PDF: http://arxiv.org/pdf/1509.01972v1.pdf
Soundbite: “Our analysis suggests that the brain estimates the reliability of the stimulus on a short time scale of at most a few hundred milliseconds.”

Brain Model of Information Based Exchange
James Kozloski
PDF: http://arxiv.org/pdf/1509.02580v1.pdf
Coolness: IBM Neural Tissue Simulator (about NTS | NTS slides | 1st article)

Interplay between the local information based behavioral responses and the epidemic spreading in complex networks
Can Liu, Jia-Rong Xie, Han-Shuang Chen, Hai-Feng Zhang, Ming Tang
PDF: http://arxiv.org/pdf/1509.01321v1.pdf
Soundbite: “The spreading of an infectious disease can trigger human behavior responses to the disease, which in turn plays a crucial role on the spreading of epidemic…. Our finding indicates that, with the increasing of the response rate, the epidemic threshold is enhanced and the prevalence of epidemic is reduced.”

Identification and modeling of discoverers in online social systems
Matus Medo, Manuel S. Mariani, An Zeng, Yi-Cheng Zhang
PDF: http://arxiv.org/pdf/1509.01477v1.pdf
Soundbite: “We develop an analytical time-aware framework which shows that when individuals make choices — which item to buy, for example — in online social systems, a small fraction of them is consistently successful in discovering popular items long before they actually become popular. We argue that these users, whom we refer to as discoverers, are fundamentally different from the previously known opinion leaders, influentials, and innovators.”

Time-aware Analysis and Ranking of Lurkers in Social Networks
Andrea Tagarelli, Roberto Interdonato
PDF: http://arxiv.org/pdf/1509.02030v1.pdf
Soundbite: “Our goal in this work is to push forward research in lurker mining in a twofold manner: (i) to provide an in-depth analysis of temporal aspects that aims to unveil the behavior of lurkers and their relations with other users, and (ii) to enhance existing methods for ranking lurkers by integrating different time-aware properties concerning information-production and information-consumption actions.”

Plain Language Summaries for Translation in Science

First posted at the Krafty Librarian blog.


translationalhand1

At MLA last May, I was walking around the vendor hall, like most of us who attended, I assume. I was on a mission, though. I stopped by every vendor table that had anything to do with publishing or translational science, and talked with them at length about the idea of having plain language abstracts. I’ve been a fan of plain language initiatives for a long time, as evidenced by our library’s Plain Language Medical Dictionary app from some years ago. I wish I could say that I was doing this as a direct result of the PNAS article on the topic published in March, but no such luck. That would have helped make my arguments more compelling, I’m sure. I found the article today, thanks to the National Science Communication Institute retweeting Len Fisher.

A circuitous route, but effective enough to reach me. The article in question was this.

Lauren M. Kuehne and Julian D. Olden. Opinion: Lay summaries needed to enhance science communication. PNAS 112(12):3585–3586. doi: 10.1073/pnas.1500882112 http://www.pnas.org/content/112/12/3585

The article was short and sweet. It talked briefly (very briefly) about alternative modes of science communication, such as social media and blogs, and how they impact on audience, understanding, and adoption of new ideas. The authors then pointed out that these are limited to the few who choose to follow that channel, and it misses the benefits and affordances of mass media channels, a concept which they illustrated with a diagram of how they perceived the connections between the information channels and the audiences. Here’s the gist of it.

Scientists communicate with the public through these channels:
1) Social media and press releases
2) Journalist contacts
3) Lay abstracts
4) Traditional abstracts

The potential audiences are:
1) Public
2) Managers and decisionmakers
3) Scientists in other fields
4) Scientists in your own field

So far so good? There are obviously many more potential audiences as you subdivide these. In my conversations I was rather fond of mentioning insurance companies and agents as critical links in the chain of adopting healthcare innovations who are perhaps more likely to benefit from a plain language abstract. I also talked about the importance of highly motivated patients who take new articles to their clinicians as a recent and influential loop in the information chain that changes practice. For benefits to come through these channels requires not simply that there be a version of the abstract that is in plain language (a lay summary) but also, and equally important, that those lay summaries not be behind a paywall. One of the publishers was absolutely sure their abstracts were not being a paywall, and then when they went to show me, well (ahem), they found they were. As in, the abstracts were locked behind a paywall. Oops.

The most important part of the article’s diagram was the very subtle sideways dashes. Where do the journalists get the hook, the info that leads them to ask more questions and write those mass media articles that reach such large audiences? What triggers the journalist to reach out for those important conversations with the scientists? Well, the press releases, of course. That’s why our organizations work so hard on them. Seeing something posted and reposted on social media is another good way to reach them. But the traditional abstract? Not so much. The traditional abstract is crafted explicitly for other scientists in your field, and only partly for scientists beyond that. Now, a lay summary, a plain language abstract, that has HUGE potential as a way to reach journalists. It’s another marketing tool, beyond being the right thing to do to help patients, or to help get science into the hands of those who actually use it, or to help influence clinical practice and foster more rapid adoption of new discoveries and treatments.

What Patients Think About Clinical Trials, Take 2 (#bioethx)

At the Doctor's Office: Push For Help

ADDENDUM

Within minutes after the previous post went live, I was contacted on Twitter by another patient advocate, Willow, also known as Serious Skeptic. She* expressed another wide area of patient concerns about clinical trials, ones that were new to me, and which deserve representation in this post, even if they aren’t from the official public #PatientChat event. Because Willow has a locked account, and I respect that, I asked her permission to share the links and the essence of some of her private tweets. The following is posted with her consent, but represents my words and distillation of what I learned from her.

Willow was concerned about ethical breaches in clinical trials, especially:
– trials that are designed specifically to promote use of a drug (marketing);
– trials that suppress undesired findings or which fail to publish or share negative findings;
– trials that don’t share their data;
– trials that don’t make relevant or useful findings available to all trial participants.

I had the impression she’d kind of like the research studies to also notify trial participants of publications that do result from their participation. I know, I do, myself, and being a medical librarian, I take notes on my research participation, the names of studies, the names of the PI, and I stalk their publications for years until I see the research in which I participated. I often ask to be alerted, and usually received some sort of polite demurral, and nothing else. I wish they had an email list I could just subscribe to for alerts from their lab.

Anyway, when Willow described clinical trials that are actually marketing ruses, my reaction was, “Whoa! Not really? Doesn’t the IRB process protect against that?” Evidently not. The concept she was describing most is called seeding trials. Here are some links she shared with me, or quotes and/or resources from those articles.


A physician is invited by a pharmaceutical company to take part in a study involving an FDA-approved drug. The physician’s responsibilities entail prescribing the drug for patients and then completing three questionnaires about each patient’s experience with the drug. The questionnaires are quite short and will take about 20 minutes each to complete. The sponsor will pay $1,500 for each completed questionnaire. The physician is very interested in participating because it looks like a great way to increase practice revenues.

Rusczek JP, Rusczek AM. Fraud and Abuse in Clinical Research: Three Case Studies. ABA Health eSource June 2010 6(10). American Bar Association. http://www.americanbar.org/content/newsletter/publications/aba_health_esource_home/Rusczek.html
– Research Involving Non-Employed Physician Investigators
– Marketing Disguised as Research
– Double Billing

The public has lacked convincing documentary evidence of a long-suspected drug company practice: promoting a new drug by sponsoring a randomized trial in which participating physicians use the drug as they follow the trial protocol. This practice—a seeding trial—is marketing in the guise of science. The apparent purpose is to test a hypothesis. The true purpose is to get physicians in the habit of prescribing a new drug.

Sox HC. Seeding Trials: Just Say “No.” Ann Intern Med. 2008;149(4):279-280. doi:10.7326/0003-4819-149-4-200808190-00012 http://annals.org/article.aspx?articleid=742309

Seeding trials are designed to appear as if they answer a scientific question but primarily fulfill marketing objectives. Kessler and colleagues (3) portrayed seeding trials as “attempts to entice doctors to prescribe a new drug being marketed by the company” while the company puts its product in the hands of practicing physicians, hoping that the experience of treating patients with the study drug and a pleasant, even profitable, interaction with the company will result in more loyal physicians who prescribe the drug (4).

Hill KP, Ross JS, Egilman DS, Krumholz HM. The ADVANTAGE Seeding Trial: A Review of Internal Documents. Ann Intern Med. 2008;149:251-258. https://www.leg.bc.ca/cmt/39thparl/session-4/health/submissions/Hill_The_Advantage_Seeding_Trial_2008.pdf

“Merck’s marketing division handled both the scientific and the marketing data, including collection, analysis, and dissemination; and Merck hid the marketing nature of the trial from participants, physician investigators, and institutional review board members.”

Keim B. Merck Vioxx Study Disguised Marketing as Science. Wired 08.19.08 1:22 PM. http://www.wired.com/2008/08/merck-vioxx-stu/

Merck minimized the true risks of Vioxx (Apr 17, 2008) https://www.youtube.com/watch?v=PQYxZSUDnqI

The maker of Neurontin disguised an effort to promote the anti-seizure drug to physicians as a clinical trial and failed to inform involved physicians and patients, according to a new analysis published Monday in the Archives of Internal Medicine journal.

Girion L. Neurontin study was a sham designed to boost drug sales, researchers say in medical journal. Los Angeles Times June 27, 2011. http://articles.latimes.com/2011/jun/27/news/la-heb-neuronton-seeding-trial-20110627

Seeding trials are an unethical, dangerous way to market a product. The IRB needs to become a better-equipped committee that can identify seeding trial practices from honest clinical trials, and the FDA needs to demand more transparency from companies sponsoring clinical trials, to better protect public health and the integrity of clinical research.

Varga M. Are Seeding Trials Ethical? Kulkarni Law Firm Blog June 11, 2012 11:11. https://www.conformlaw.com/blog/are-seeding-trials-ethical/

Recommended Principles to Guide Academy-Industry Relationships. American Association of University Professors. University of Illinois Press, Jan 25, 2014. See the endnotes on pages 341-2. https://books.google.com/books?id=lFSNAgAAQBAJ&pg=PA341&lpg=PA341&dq=drug+seeding+trials&source=bl&ots=AEZ1Xa7NUS&sig=W_nCm_h2w7Uhtf5tWd4V6sf5ggI&hl=en&sa=X&ved=0CDIQ6AEwAzgeahUKEwjw9JWVyovGAhWjWowKHTvgAJQ#v=onepage&q=drug%20seeding%20trials&f=false


Because of the risks and distrust generated by the practice of seeding trials, Willow suggested that it might be wiser to wait to test new meds on your own body until they’ve been out for a few years, unless you are so ill that you have no alternatives. Now, of course, if everyone does that, then there are NO NEW DRUGS because we can’t test them! And that is a situation in which we all lose.

My own choices? I take risks that I won’t ask others to take. I try to be informed about the risks I take. When I participate in a research study, I ask a lot of questions, and I pay very close attention to my body. If my canary-in-the-mine body complains, I withdraw from the study. Well, I would. So far, I’ve never actually needed to withdraw from a research study, but I have ceased taking actual FDA-approved meds prescribed for me that my body couldn’t handle. I’m hoping that the #bioethx chat group will pick up on this topic next, and hoping they can find an invited speaker to talk about what IRB committees have done and are doing to try to address this, to build confidence in medical research.


* I am assuming Willow is a she because I interpret the name Willow as a female name. I have no knowledge or confirmation of that, and it isn’t any of my business anyway. I am using the female pronoun to describe her simply for convenience, and intend no disrespect.


ADDENDUM TWO, June 13

A few clarifications and corrections from the ever thoughtful Willow.

Willow feels my concern about limiting drug discovery isn’t valid, since seeding trial occur for drugs that are already patented. My concern is that fear of seeding trials will scare some participants off of drug trials entirely. Drug discovery trials are legitimate, but the problem remains that it can be difficult to distinguish discovery trials from seeding trials, since the physicians and patients are both kept in the dark by the drug manufacturers.

Hashtags of the World (HOTW): #WhatIfResearchKit / What If Research Kit … ?

Apple ResearchKit
Apple ResearchKit: https://www.apple.com/researchkit/
ResearchKit for Developers: https://developer.apple.com/researchkit/

Last week, while I was deep in the throes of a family crisis, Apple announced “ResearchKit.” I noticed it, but obviously had no time to do anything with it. I’m looking forward to exploring that. I mean, really, it’s getting a ton of press!

9to5Mac: ResearchKit did in 24 hours what would normally take 50 medical centers a year – Stanford University

Bloomberg Business: Thousands Have Already Signed Up for Apple’s ResearchKit

CNBC: Apple’s ResearchKit: Gamechanger for digital health care?

Forbes: Apple’s Open-Source ‘ResearchKit’ And The Future Of Medical Research

MacWorld: First medical apps built with Apple’s ResearchKit won’t share data for commercial gain

MacWorld: Stanford’s ResearchKit app gained more users in 24 hours than most medical studies find in a year

TechCrunch: ResearchKit An “Enormous Opportunity” For Science, Says Breast Cancer Charity

TedBlog: mPowering the Apple ResearchKit: How Max Little put a Parkinson’s app on the iPhone

TheVerge: Apple’s new ResearchKit: ‘Ethics quagmire’ or medical research aid?

TheVerge: Apple’s new ResearchKit lets iPhone users participate in clinical trials; It could help researchers recruit from more diverse populations

Wired: Apple’s ResearchKit is a New Way to do Medical Research

Here is what Apple and it’s current group of partners are envisioning for how ResearchKit might be used. It sounds pretty inspiring already, with a nod to some of the complicated ethical and privacy issues poised to emerge.


ResearchKit – how iPhone is transforming medical research https://www.youtube.com/watch?v=VyY2qPb6c0c

In the meantime, several of my friends and colleagues on Twitter have begun discussion their visions for what could be done with ResearchKit. This group includes patients as well as researchers, and this, I suspect is the demographic, the community creating collaborations where the most profound and productive changes will be found. Here’s what they are saying, so far. Why don’t you join in?

Why stop there? What other possibilities could come from widespread adoption and use of ResearchKit?

#WhatIfResearchKit helped monitor the progression of Alzheimer’s Disease. Like a more official version of what was seen in ‘Still Alice’?

#WhatIfResearchKit helped improve treatment and intervention for depression through passive activity tracking?

#WhatIfResearchKit apps were developed in collaboration with the patient community? If these apps aren’t used, there’s no data to analyze.

What if Apple released a tool so anyone could make a #ResearchKit connected app. True citizen science. #WhatIfResearchKit

What if a community of translator helped translate #ResearchKit studies and consent information into other languages. #WhatIfResearchKit

#WhatIfResearchKit was rolled into the #PrecisionMedicine initiative and the NIH took a more open-source mentality to data collection.

That #WhatIfResearchKit already exists recalls @rufuspollock: “The best thing to do with your #data will be thought of by someone else.”

#WhatIfResearchKit tracked child development so that children with autism could be diagnosed quicker and provided with skills

Catching up on two rich threads: #bcsm + #WhatifResearchKit Who says we can’t cry and laugh and hope and rage all at the same time?

#WhatIfResearchKit was a cross-platform non-profit initiative partnering together device manufacturers to better healthcare? #DigitalHealth

“The key to understanding #health & disease is research & data.” Check out @AppIeOfflciaI’s #WhatIfResearchKit: http://apple.co/1FFSLR8

#WhatIfResearchKit JMIR will built a Healthbook app which randomizes participants to #mhealth apps #megatrial with 700 million participants

Healthbook http://www.healthbook.com/ will use #researchkit and also support n-of-1 trials to evaluate #mhealth apps #WhatIfResearchKit

What if all the people who are “healthy” (for now) could contribute their data as controls? #WhatIfResearchKit

#WhatIfResearchKit had an opt-in for every human, to proxy any slice of my data to #opensource science. +audit-trail

#WhatIfResearchKit was my life baseline, always collecting data when I’m healthy, so when I’m sick, the record is computable + comparable.

#WhatIfResearchKit was available on android platforms to ensure more socioeconomic, racial and ethnic diversity of participants

#WhatIfResearchKit flipped the paradigm community based studies studying access to care, how tertiary care centers impact POC communities

What if Apple made a dashboard so that we could all see enrollment numbers for #ResearchKit apps (in real time)? #WhatIfResearchKit

Reporters: If you are writing about #ResearchKit check out the ideas being shared here: #WhatIfResearchKit (and interview those innovators)

#WhatIfResearchKit – A story in 140 character bursts of hope https://storify.com/iamspartacus/whatifresearchkit … via @iam_spartacus