Regulating Curators?

This article suggests that a new bill in introduced in California may regulate how the modern curators and interpreters of biomedical data (bioinformaticians) may end up being regulated and tarred by the same brush as direct-to-consumer genetics testing companies.

“This law doesn’t just cover companies, it covers what’s done in academic institutions, too,” Butte said. “Nothing in this bill blocks that.”

More evidence, in any case, of the centrality of information processing to the biomedical enterprise.

Never Ending STories

In preparation for a conference on substitutable platforms in health IT, I was directed to an instance of a growing form of self-publication that we call the Never Ending STory (NEST). This instance of NEST is the knol which has become an increasingly popular venue for publications including ones that look a lot like standard peer reviewed journals. More generally, a NEST starts as an embryonic paper. With iteration and with the help of co-author and reader suggestions, it incubates a mature manuscript. Unlike a blog, it is not just a snapshot of a narrative perspective in a sequence of snapshots, but a single integrated document. Unlike a wikipedia article it does not claim encyclopedic authoritativeness (or at least sole authoritativeness so that disagreeing contributors have to battle it out) but only the moderated perspective of the authors. Unlike a standard peer review article, it's publication does not signify the end of its incubation and the hatching of a fully mature narrative. And it is timely and time efficient to make NEST's more prevalent. How often, have you read a scientific article from five years ago and wondered if more recent developments had influenced the authors' perspective on their prior results and/or conclusions? Would it not be more effective to allow the author to update their articles (while maintaining an archival history of all prior versions) so that they continue to be current? Or if there were additional data that bolstered the case of the original article, the author could add these data to that article without having to go through an entire process of a new publication just for the incremental data. That would reduce unnecessary publication noise and increase the value of the article to the reader.

Although, right now, we are using the knol as the infrastructure for our NESTs, we can hope that academic publishers will provide vehicles of similar functionality. Until, then we will just have to incubate our own.

Once we have electronic medical records implemented, what then?

We, as nation, are in the process of investing several billion dollars into the implementation of electronic health records. If all goes well, there will be a lot of individual data buried in these care systems. This begs the question of what utility, if any, this data has for research whether for genomics, comparative effectiveness research, pharmacovigilance, or public health. The NIH is hosting a conference at the end of October (entitled “Widening the Use of Electronic Health Record Data for Research”) to attempt to answer the question. All are interested parties are invited.

Evolution of Evolution

In a mashup of bioinformatics methods and historical scholarship Ben Fry provides an artistic rendering of the evolution of Darwin's work. Watch it evolve for a few minutes.

Hat tip: Ben Adida

The Least Publishable Unit

This might explain why we have so many journals too.

Hat tip: Ben Adida

What are medical libraries expected to do?

This is not an abstract question about the future of libraries, although that is also an interesting question. It is a question about what the medical school accrediting organizations have determined. "The Liaison Committee on Medical Education (LCME) is the nationally recognized accrediting authority for medical education programs leading to the M.D. degree in U.S. and Canadian medical schools. The LCME is sponsored by the Association of American Medical Colleges and the American Medical Association." and this is what they had to say (the bold face is mine for emphasis):

D. Information Resources and Library Services
ER-11 The medical school must have access to well-maintained library and information facilities,
sufficient in size, breadth of holdings, and information technology to support its education and
other missions.

There should be physical or electronic access to leading biomedical, clinical, and
other relevant periodicals, the current numbers of which should be readily
available. The library and other learning resource centers must be equipped to
allow students to access information electronically, as well as to use self-instructional
materials.

ER-12 The library and information services staff must be responsive to the needs of the faculty, residents
and students of the medical school.

A professional staff should supervise the library and information services, and
provide training in information management skills. The library and information
services staff should be familiar with current regional and national information
resources and data systems, and with contemporary information technology.
[Revised annotation approved by the LCME in October 2007 and effective immediately.]
Both school officials and library/information services staff should facilitate access
of faculty, residents, and medical students to information resources, addressing
their needs for information during extended hours and at dispersed sites.

(This is taken from:
http://www.lcme.org/functions2008jun.pdf found at:http://www.lcme.org/standard.htm
Hat tip David Osterbur.)

These are important recommendations and ones which foreshadow trends from the very near future. We have embraced this educational mission from access of electronic resources to teaching biomedical researchers how to perform bioinformatics-enabled research (see the bioinformatics nanocourses offered to all by Reddy Galli— details here ). The central question is whether librarian training will embrace the information technology that will be required to keep libraries current and relevant to their patrons. The answer to that question will determine where the future librarians are trained and that will in turn determine how central libraries remain to the academic mission.

The alien within and other tales of curatorial genetic mishap

As reported by the New Scientist.

Another quality improvement challenge for the genomically-knowledgeable librarian.

Different cell, different story

A Swiss-American collaboration makes vivid just how specific the effect of cellular/tissue context is upon the impact of genetic variation. We have understood for several years that each tissue has a different (if highly overlapping) mix of expressed genes (mRNA). However this study shows, in a study of three different cell types in 75 individuals, that the variation in expression between individuals that is attributable to genetic variation in control elements (i.e. regulatory SNP's) is highly tissue dependent. That is, over half of the regulatory variants only have impact in particular tissues. This suggests that understanding the impact of human genetic variation will take a lot more detailed study and not only in one tissue (usually blood).

[Dimas, A.S., Deutsch, S., Stranger, B.E., Montgomery, S.B., Borel, C., Attar-Cohen, H., Ingle, C., Beazley, C., Arcelus, M.G., Sekowska, M., Gagnebin, M., Nisbett, J., Deloukas, P., Dermitzakis, E.T. and Antonarakis, S.E. (2009) Common Regulatory Variation Impacts Gene Expression in a Cell Type-Dependent Manner, Science.]

Distortions, biases, amplification and invention in the biomedical literature.

The telephone game that many of us played as children showed the amusing side of how indirect communication can lead to distortion of the original message. Steve Greenberg has written an eye opening article in the British Medical Journal describing how he followed the entire citation network for a particular claim (that β amyloid, a protein accumulated in the brain in Alzheimer’s disease, is produced by and injures skeletal muscle of patients with inclusion body myositis) that in a medical analog of the telephone game resulted in the subsequent adoption of questionable "facts" as medical conventional wisdom. He also shows how, much like websites trying to increase their Google Pagerank, there arise mutual citation networks that will increase the acceptance of their joint claims. One of the lasting contributions of this study is the development of a vocabulary of citation distortions (reproduced below) that Greenberg used to taxonomize the citation network. It also is a vocabulary that other conscientious reviewers and readers can use in their own disciplines to identify and name these distortions.

Vocabulary of citation distortions

Citation

Both scholarly and social forms: the scholarly form connects statements to the broader

medical literature, the social form (social citation) includes self serving and persuasive

subtypes

Citation distortions

Self serving citation is always a distortion

Persuasive citation may be necessary to communicate new, sound claims to the scientific

community; it may, however, have distorted uses—citation bias, amplification, and

invention

Citation bias

Systematic ignoring of papers that contain content conflicting with a claim

Bolster claim; justifying animal models to provide opportunities to amplify claim

Amplification

Expansion of a belief system without data

Citation made to papers that don’t contain primary data, increasing the number of

citations supporting the claim without presenting data addressing it

Invention

Citation diversion—citing content but claiming it has a different meaning, thereby diverting

its implications

Citation transmutation—the conversion of hypothesis into fact through the act of citation

alone

Back door invention—repeated misrepresentation of abstracts as peer reviewed papers to

fool readers into believing that claims are based on peer reviewed publishedmethods and

data

Dead end citation—support of a claim with citation to papers that do not contain content

addressing the claim

Title invention—reporting of “experimental results” in a paper’s title, even though the paper

does not report the performance or results of any such experiments

Accidental Neurosurgery

An interesting footnote for one of the more famous inhabitants of the Countway's Warren Museum.

Another perspective from the Boston Globe.

Celebrity-driven education

Here's an interesting angle in promoting health literacy by two of my colleagues.

When does an electronic medical record look like an iPhone?

Almost never. But it could be a lot more, as articulated by several of us who recently gathered at the Countway to discuss the matter.

Public Proponents Proliferating

I was recently reviewing research on the costs of recruiting subjects for population studies. I found that even with several million dollars of subscription costs paid by the University per year, about 1/3 of the articles I had identified were not covered by our subscriptions. These articles then required an additional $20 to $35 personal investment each if I wanted to see their details. For less well-endowed institutions, the challenge is even more significant for their faculty and students. In this context, it is heartening to read this report from the Public Library of Science organization. Not only have they published high quality articles but they have 5.4 million readers, 26,000 authors, 13,000 peer reviewers, over 11,000 articles submitted in 2008 and they project that 90% of operating expenses will be covered by the PLoS funding model by the end of 2009. Hats off to a daring and creative act of social and academic organization.

A statistical cure for the voodoo

A recent issue of Perspectives in Psychological Science demonstrates the kind of full-throated give and take that makes for better science. An article by Ed Vul et al, questions the results of functional magnetic resonance imaging (fMRI) studies that relate imaged changes to personality traits, emotional states, and social interactions. The heart of the critique is how the correlations are calculated and how their statistical significance is reported. Their analysis is backed up with a very substantial survey of the investigators of the studies in question. In the same issue, the supporters and detractors of the critique are given their say. Most impressive is the statistical perspective of Lindquist and Gelman. It is even-handed and informative and should be required reading for any student about to engage in research of the increasingly familiar "high dimensionality" data sets (e.g. in genomics and imaging) that allow a multiplicity of questions to be asked or hypotheses to be tested.

Update: 7/7/2009: Nice piece on this topic from NPR.

Minting a new medical record

Early on in the development of personal health records, we had many discussions about how to jump-start the critical first step to adoption: populating that personally controlled record with clinical data. We recognized that, especially in the early years (i.e. 1994) healthcare institutions might be loathe to share data of their patients with these same patients (in electronic form) and even less so with other institutions delivering health care. So, it was with a slightly evil gleam that we considered the following opportunity when some of the local healthcare institutions developed patient portals to their healthcare systems (e.g. PatientSite and Patient Gateway). If patients could access their own medical record at one or more institutions, then a program working on their behalf (using their credentials) could then automatically log in and scrape up whatever HTML-formatted data was available and then reformat it into a standardized data model within a truly portable and personally controlled health record. This solution would not require that any institution hew to a particular data standard or communication protocol (beyond HTTP and HTML) but it would require us to be very nimble to update our translation programs. Specifically, if one of the hospitals would change the formatting of the screens on the patient portal, we would have to change the program that transforms those screens into a useable personal health database. That would certainly have been possible and legal but we decided not to proceed out of a sense of collegiality with our medical informatics colleagues and instead worked to cultivate more explicit data sharing governance and agreements.

Recently, however, I was reminded by my colleague Jeff Behrens, of a very successful model of data sharing in a personally controlled financial record: Mint.com. It's a remarkable site that allows anybody (and without additional cost) to develop a cohesive view of their finances drawn from myriad information sources including: your bank account(s), your retirement accounts (e.g. 401K plan), your investment brokerage account, your credit/debit card(s), and your mortgage account. To just name a few. This in the absence of any data interchange model across this multiplicity of institutions and functions. Once this aggregation is performed for you, many services are available such as alerts for over-budget spending, due dates of credit card bills, changes in your spending mix, and decision support for improved financial performance (e.g. switching to lower interest credit cards—Mint.com knows the interest rates on each card). There are a few remarkable properties of this site that may be quite instructive for healthcare information technology.

• Some of us are quite comfortable passing along all our account information, user names, and passwords to a third party given a basic level of confidence in their privacy policy, as backed up by their explicitly state policies.
  • Essential to this comfort however, is the immediate value that the user obtains by participating. Not in the distant future but today.
• Hundreds of data sources of relevance are unified without a single standard data model (unless you consider Mint.com's model the standard).
• The data source institutions did not enter into an agreement for data sharing. Only the consumer had to agree to let Mint.com automatically access these data sources with their borrowed credentials.
• A national data sharing infrastructure was created in 1 year from a startup-sized technology development and marketing budget.

Mint.com now has over a million users and is tracking over $50 billion in transactions. Can healthcare organizations, or the government or healthcare entrepreneur catalyze an analoguous success?

iPhone vs. Blackberry

So many of our colleagues appear to be doing their daily work holding onto an electronic device carefully positioned below eyesight (barely) that this direct comparison of two leading mobile platforms may be useful. Alternatively, there are ways to make meetings more efficient and personal.

Open Source Software Not So Evil

I recall several earnest conversations with colleagues who insisted that by making all the projects I was involved in (e.g. i2b2 and Indivo) adhere to an Open Source license, I was being both naive and counterproductive. There was no way, I was told (as recently as last year) that "real" companies would get anywhere close to supporting products that had an Open Source license. This story about Microsoft's use of Open Source software in its search engine developments should settle those concerns, at least for the next few days.

More here.

Masters of Sex

When studies that helped fuel the sexual revolution become the subject of scholarly retrospectives, one has to wonder what is the current social aphrodisiacal locus?


Critically acclaimed biographer Thomas Maier will be at the Countway Library of Medicine for a presentation and signing of his newest release, The Masters of Sex, offering an unprecedented look at William Masters and Virginia Johnson, the nation’s top experts on sex; their pioneering studies of intimacy, and the sexual revolution they inspired.
Thursday, May 14, 2009, Minot room, Countway Library
4:30 pm: PRESENTATION
5:30 pm: BOOK SIGNING
(The Harvard Medical Coop will be selling the book at Countway)
5:30 RECEPTION: Lahey Room

What Open Access Might Be Competing With

There has been some concern articulated about the bias that could arise from author-fee-driven publications (which is one flavor of open access). Here is an example of bias within the closed access framework that can arise almost completely undetected (thanks to The Scientist for the pointer) and enabled by an industry:industry collaboration

The Australasian Journal of Bone and Joint Medicine, which was published by Exerpta Medica, a division of scientific publishing juggernaut Elsevier, is not indexed in the MEDLINE database, and has no website (not even a defunct one). The Scientist obtained two issues of the journal: Volume 2, Issues 1 and 2, both dated 2003. The issues contained little in the way of advertisements apart from ads for Fosamax, a Merck drug for osteoporosis, and Vioxx. (Click here and here to view PDFs of the two issues.)

Hat tip Josh Parker

Addendum 5/8/2009 here.

5/10/2009 More from The Scientist.

From Moss to Autism to Skateboarding

Our very own Dennis Wall, demonstrates some of his impressive extracurricular "skillz."