Blast from the not so distant past – special issue of JMBE on Scientific Ethics

So _ picked up my new issue of Microbe in the mail today and I saw something in it that seemed very intriguing.

A whole section of JMBE – the Journal of Microbiology and Biology Education dedicated to Scientific Ethics.  Sounded intriguing.  So I looked it up.  Took a bit to find it but there it was from December 2014 – Volume 15 number 2

I don’t know about the specific articles but the whole collection seems definitely worth a look and of potentially many uses.

So I have listed the individual papers below.  Kudos to ASM and JMBE for putting this together.  Now off to read some of the papers.

Some notes on "Citations for Sale" about King Abdulaziz University offerring me $$ to become an adjunct faculty

There is a news story in the Daily Cal titled “Citations for Sale” by Megan Messerly about King Abdullah University King Abdulaziz University trying to pay researchers who are highly cited to become adjunct professors there to boost their rankings.  This article stemmed from a blog post by Lior Pachter.  I was interviewed by the Daily Cal reporter about this because I had sent Lior some of the communications I had had with people from KAU where they tried to get me to do this.
I am posting here some of the email discussions / threads that I shared with Lior and Megan.
Thread #1.
Here is one thread of emails in which KAU tried to get me to become an Adjunct Professor.  I have pulled out the text of the emails and removed the senders ID just in case this would get him in trouble.
Received this email 3/6/14

Dear Prof Jonathan, 

How are you? I hope every thing is going well. I hope to share work with you and initiate a collaboration between you and me in biology department, Kind Abdulaziz university . My research focuses on (redacted detail). I hope that you would agree . 

Redacted Name,Ph.D
Assistant Professor, Faculty of Sciences, King Abdulaziz University, Jeddah, KSA.

My response:

What kind of collaboration are you imagining?

His response:

Hi Prof Jonathan, 

Let me to explain that the king abdulaziz university initiated a project which is called Highly Cited Professor ( HiCi). This project can provide a contract between you and our university and from this contract you can get 7000 US$ as a monthly salary .So  this project will allow you to generate two research proposal between you and a research stuff here in order to make an excellent publications in high quality journals as you always do. 

I hope that I was clear. I’ m looking forward to hear from you. Finally, I think that a very good chance to learn from you. 

 Another email from him:

Dear prof Jonathan, 

I’ d like to tell that Prof Inder Verma will come tomorrow to our university  as a highly cited professor and he also signed a contract with us. At March 28 Prof Paul Hebert will come to our university and we actually generated two projects with Prof Paul. I hope you trust me and you call Prof  Inder and  Paul to be sure. 

From me:

I trust you – just am very busy so not sure if this is right for me
Sent from my iPhone

From him:

You will come to our university for just two visits annually and each visit will take only  one week. Take you time to think. Bye

Another email from him

Seat Dr Jonathan, 

What is your decision?

My response:

You have not really provided me with enough information about this.

From him:

Well, you will sign a contract as a highly cited professor between you and KAU. if it happen you will get 7,000 US$ per month for one year as a salary.  From  this project you would be able to generate two proposal with around 200,000 US$ and you will get incentives from each one. In the further we can initiate a mega project with 1.5 million US$.   Is that clear? 

From me:

I could use a formal , legal description of the agreement that one is expected to sign 

From him:

You can ask Prof Dr. Inder Verma he is now in my department and he did two presentation today. Also you can ask my professor prof  Paul Hebert, biodiversity institute of Ontario who will come to my department in March 28,2014.

From him:

if you would agree . Coul you please provide me with your CV with list of publication? 

From him:

Are you agree or no?

From me:


You have not provided me with anywhere near enough info to evaluate this 

Do you have any legal agreement I can look at?

From him:

Agreement from KAU
without providing me with your CV I could not be able to talk to university administration. I told you before ask under verma or Paul Hebert both of them have contract. Dr verma ” editor in chief of PNAS who is left KAS since 4 hours ago. Finally, its up to.

From me:

No thanks
Not interested from what you have told me

Thread #2
Received this email on 12/17/13

Dr. Mansour Almazroui
to jaeisen
Dear Prof. Jonathan Eisen ,

I am Dr. Mansour Almazroui, Highly Cited Program Manager, at King Abdulaziz University (KAU), Jeddah, Saudi Arabia. On behalf of KAU with great pleasure, I would like to invite you to join our innovative collaboration program that is called “International Affiliation program”.

KAU is considered as the largest university in the region serving more than 150,000 students, with around 4,000 faculty members and 30 colleges. For more information please locate us at:

The envisaged program aims to elevate our local research activities in various fields. We only extend our invitation to highly ranked researchers like you, with a solid track record in research and publications to work with KAU professors.

Joining our program will immediately put you on an annual contract, as a Distinguished Adjunct Professor. In this regard, you will only be required to work at KAU premises for three weeks in each year of your contract.

We hope you to accept our invitation and looking forward to welcome you.  Please don’t hesitate to contact me for any further query or clarification.


Dr. Mansour Almazroui
Highly Cited Program Manager,
Office of the Vice President for Graduated Studies and Research,
King Abdulaziz University (KAU).
Director, Center of Excellence for Climate Change Research
King Abdulaziz University
P. O. Box 80234, Jeddah 21589,
Saudi Arabia

I wrote back

I am intrigued but need more information about the three weeks of time at KAU and the details on the contract. 

Jonathan Eisen  

Sent from my iPhone

Got this back

Dear Prof. Jonathan Eisen , 

Hope this email finds you in good health. Thank you for your interest. Please find below the information you requested to be a “Distinguished Adjunct Professor” at KAU. 

1. Joining our program will put you on an annual contract initially for one year but further renewable. However, either party can terminate           its association with one month prior notice.
2. The Salary per month is $ 6000 for the period of contract.
3. You will be required to work at KAU premises for three weeks in each contract year. For this you will be accorded with expected three         visits to KAU.
4. Each visit will be at least for one week long but extendable as suited for research needs.
5. Air tickets entitlement will be in Business-class and stay in Jeddah will be in a five star hotel. The KAU will cover all travel and living             expenses of your visits.
6. You have to collaborate with KAU local researchers to work on KAU funded (up to $100,000.00) projects.
7. It is highly recommended to work with KAU researchers to submit an external funded project by different agencies in Saudi Arabia.
8. May submit an international patent.
9. It is expected to publish some papers in ISI journals with KAU affiliation.
10. You will be required to amend your ISI highly cited affiliation details at the ISI web site to include your employment and         affiliation with KAU.   

Kindly let me know your acceptance so that the official contract may be preceded.

I promtly forwarded this to my brother with a note:

One way to make some extra money … Sell your reputation / ISI index  

Sent from my iPhone

And my brother eventually shared this with Lior  …
UPDATE 1: 12/5/2014

One key question is – what are the rules and guidelines and ehitcs of listing affiliations on papers.  Here are some tidbits on this

From Nature Communications:

The primary affiliation for each author should be the institution where the majority of their work was done.

From Taylor and Francis

The affiliations of all named co-authors should be the affiliation where the research was conducted.


Present the authors’ affiliation addresses (where the actual work was done) below the names.

UPDATE 2: Some other posts of relevance

UPDATE 3: A Storify

Strange email of the week: "Publication Integrity and Ethics"

Just got this email that I have pasted below. This seems very very strange. Something is amiss here I think but not sure what. Anyone out there know anything about this?

You are invited to join the Publication Integrity and Ethics (herein referred to as PIE) as one of its founding members. PIE, a not-for profit organisation, offers free membershipto all interested individuals. Please join us and become part of this exciting new movement in the world of publishing ethics: (for standard membership) (for editor-in-chiefmembership)
As a founding member you will play a central role in shaping the organisation; you will benefit from the many and varied facilities the PIE organisation provides in the world of publishing and ethics. This includes its own guidelines and code of conduct for all membership categories, regular updates in the field, newsletters, e-learning with online exercises and access to our sub-committee’s database. The complaint’s section allows members and adherents to raise issues, regarding any possible breach in the code of ethics and integrity in the publishing sector. PIE provides advice and represents members and adherents freely; it aims to deal with complaints in an ethical manner and resolve them promptly.
As part of the commitment to being a member-led, UK-wide and world-wide organisation, PIE intends to identify regional leads to promote the society and ensure that it remains diffuse, responsive and reflects the publication integrity and ethics priorities across the UK and with a global outreach. Members are invited to take part in a shaping PIE by directly communicating with the PIE’s council and other members with regards to the many issues related to this field; they may issue specific guidelines which can be communicated with other national and international organisations.
PIE is able to recommend short online courses, online diplomas and advanced diplomas to its members; these are specifically related to the integrity and ethics in publication and research, law and medical ethics, research governance, strong ethical practice and management. The course title, description and link to the course registration are usually posted on the PIE’s website as a service to our members.
Our online member’s and adherent’s directory is a valuable asset and will allow communications and collaborations between authors, editors, publishers, scientists and a variety of academics in shaping and advancing  the world of publishing ethics in the service of humanity.
We welcome you to being part of the PIE family. Tim ReevesThe Publication Integrity & Ethics CouncilLondon, United Kingdom

Update 10 AM 11/26: Ivan Oransky at Retraction Watch has a post with information about PIE

Update 8 AM 11/27: Neuroskeptic has posted a detailed investigation of PIE.

HeLa genome sequenced w/o obtaining permission/consent from family – some comments and background

Last week David Coil in my lab reminded me that he had been wanting to borrow a copy of “The Immortal Life of Henrietta Lacks” by Rebecca Skloot.  I have read the book many many times and had told David I even had a preprint that Skloot or her publicist sent me before the book came out (I did not know Skloot then – I just got it because of my blog).  As I went to grab the preprint off my shelf in my office he said he wanted to read it know because the genome of the HeLa cells which had been taken from Mrs. Lacks had been published a few days before.  I was shocked.  I asked him if he knew if the authors of said paper had gotten consent before publishing it.  So I opened a web browser and googled and found the paper and some news stories and a press release from the group who did the sequencing.

Holy fuck.  They did not seem to have permission.  Uggh.  I had thought about this a lot because a few years ago I was thinking of writing a review of “The Immortal Life of Henrietta Lacks”. As part of that started to write about the possibility of sequencing the HeLa genome and what that might mean.  I also did an April Fools joke relating to the topic:  And every time new sequencing technology comes along I have thought about – and discussed with others – the possibility of sequencing the HeLa genome.  And every time I got to this point I decided that it would be unethical, inappropriate, and downright stupid to do this without consent.  Note – my original plans for the book review involved a focus on the strange balance between openness and sharing in the history of HeLa and the lack of consent (e.g., see this blog post).

I was so angry about the lack of consent here that I took to Twitter.


And after that there was remarkably little discussion of the issue by others. What the fuck? People get up in arms about all sorts of minor things so why not get up in arms about this? Where were all the supposed genomic ethicists out there? How did this happen? Thankfully, yesterday a piece on the topic came out from Rebecca Skloot (it was in this mornings New York Times) and it has launched this issue into a much more public discussion. So much discussion that I decided to storify it. See below.

//[View the story “#HeLa genome sequenced w/o consent (by Jonathan Eisen)” on Storify]

Lots of discussions going on out there. And I think Rebecca deserves credit for writing this piece and bringing the story out more. I tried to get people going on Twitter and it was a slog — people did not seem that interested to be honest. Now – everyone seems interested. Including some who say they agree with Rebecca (and me) that it was a mistake to publish this genome.

Alas, am wondering what these people thought before the Skloot article. Why did so many people just stand by and say nothing? Too busy? Did not occur to them that this could be an issue? Or something else.  Oh – and why did it not occur to Francis Collins and all the people behind encode that this could be an issue. They published a lot of genomic data from HeLa cells and never once asked for consent or apparently even thought about it.

Anyway – it’s about time we as a community got off our butts and started discussion how to deal with the ethics of personal genome data.  This data will be coming out more and more.  We need to figure out how to handle it and the consent issues around it.  And we also need to do a better job of figuring out what to do with samples for which consent was not given but which are used.  Should we stop using HeLa cells?  Possibly.  If we want consent to use them – who will give it?  I don’t know the answers.  But I do know one thing – science should not simply proceed forward just because these questions are hard to answer.  Publishing the genome without consent or talking to the family was a very very very bad idea given that the ethical issues around consent here are murky.

UPDATE – 5 PM 3/24/13

Adding some notes about the press release and genome publication
Genome paper: – some key quotes of interest
  • Abstract
    • “To date, no genomic reference for this cell line has been released, and experiments have relied on the human reference genome”
    • “Our results provide the first detailed account of genomic variants in the HeLa genome, yielding insight into their impact on gene expression and cellular function as well as their origins.”
  • Results
    • “produced nearly 1 billion reads of length 101 nt” (thus they produced 101 billion bases of DNA sequence information).
    • The read data are available in the European Nucleotide Archive (ENA) database under the accession number ERP001427. 
    • We report a compendium of genomic variation (CN, SNVs and SVs) as well as the first HeLa genome draft, which are available as VCF and FASTA files respectively 
    • We provide a tool to perform the translation of coordinates between GRch37 and our HeLa reference, 
    • Most variants in these HeLa cells thus represent common variants in the human population. The African-American population (to which Henrietta Lacks belonged) is spread between the African and European clusters, with the HeLa sample overlapping both. This demonstrates that although the genomic landscape of HeLa is strikingly different from that of a normal human cell, the population-specific SNV patterns are still detectable. 
  • Discussion
    • Since the establishment of the HeLa cell line in 1952, it has been used as a model for numerous aspects of human biology with only minimal knowledge of its genomic properties. Here we provide the first detailed characterization of the genomic landscape of one HeLa line relative to the human reference genome 
Original press release (a copy of which I found here)
  • “The results provide the first detailed sequence of a HeLa genome,” explain Jonathan Landry and Paul Pyl from EMBL, who carried out the research. “It demonstrates how genetically complex HeLa is compared to normal human tissue. Yet, possibly because of this complexity, no one had systematically sequenced the genome, until now.”
  • “The HeLa genome had never been sequenced before, and modern molecular genetic studies using HeLa cells are typically designed and analysed using the Human Genome Project reference. This, however, misrepresents the sequence chaos that characterises HeLa cells, since they were derived from a cervical tumour and have since been adapting in laboratories for decades.”
  • “The study provides a high-resolution genetic picture of a key research tool for human biology. It highlights the extensive differences that cell lines can have from the human reference, indicating that such characterisation is importa for all research involving cell lines and could improve the insights they deliver into human biology.”
  • Can we infer anything about Henrietta Lacks or her descendants from this sequencing?
    • No, we cannot infer anything about Henrietta Lacks’ genome, or of her descendants, from the data generated in this study. Firstly, the subtype of HeLa cells sequenced in this study has spent decades in labs, dividing and thus undergoing mutations and changes – they are very different from the original cells that started growing in 1951. Secondly, these initial HeLa cells were taken from Henrietta Lacks’ cervical cancer tumour – as cancer is a disease of the genome, the DNA of cancer cells is usually different to that of the patient. Without any genetic information from the tumour or from Henrietta Lacks, it is impossible to distinguish which parts of the genome sequenced here originate from Mrs. Lacks, her tumour, or laboratory adaptation. The goal of this study was not to gain insights into Henrietta Lacks’ cancer or personal biology, but rather to provide a resource for researchers using HeLa cells.

UPDATE 3: 11: 40 PM 3/25/13 Presidential Commission

Rebecca Skloot has unearthed a report from the Presidential Commission on for the Study of Bioethical Issues which few people seem to have been aware of (I have heard nothing about it). 

The report was release on October 2012 but got very very little coverage and I have never seen/heard it mentioned anywhere. But it covers a lot of ground of direct relevance to this HeLa story. The whole report is available here. Here are some choice statements (bolding by me)

“Large-scale collections of genomic data raise serious concerns for the indi- viduals participating. One of the greatest of these concerns centers around privacy: whether and how personal, sensitive, or intimate knowledge and use of that knowledge about an individual can be limited or restricted (by means that include guarantees of confidentiality, anonymity, or secure data protec- tion). Because whole genome sequence data provide important insights into the medical and related life prospects of individuals as well as their relatives who most likely did not consent to the sequencing procedure—these privacy concerns extend beyond those of the individual participating in whole genome sequencing. These concerns are compounded by the fact that whole genome sequence data gathered now may well reveal important information, entirely unanticipated and unplanned for, only after years of scientific progress.”

“Whole genome sequencing dramatically raises the privacy stakes because it necessarily involves examining and sharing large amounts of biological and medical information that is not only inherently unique to a single person but also has implications for blood relatives. Genomic information is inherited and determines traits like hair and eye color. Unlike a decision to share our hair or eye color, which does not reveal anything about our relatives that is not observable, a decision to learn about our own genomic makeup might inadvertently tell us something about our relatives or tell them something about their own genomic makeup that they did not already know and perhaps do not want to know. More than other medical information, such as X-rays, our genomes reveal something both objectively more comprehensive and subjectively (to many minds) more fundamental about who we are, where we came from, and the health twists and turns that life might have in store for us.”

Because whole genome sequence information directly implicates relatives, psychological harms often are not limited to the person whose genome is voluntarily being sequenced and publicly disclosed. Even individuals who learn that they do not carry a harmful variant may experience “survivor’s guilt” if another family member is affected.”

“At the same time, individuals have a responsibility to safeguard their privacy as well as that of others, by giving thoughtful consideration to how sharing their whole genome sequencing data in a public forum might expose them to unwanted incursions upon their privacy and that of their immediate relatives. To be indifferent to the implica- tions of disclosure of sensitive data and information about one’s self is to act irresponsibly. That being said, it can be good and virtuous to share sensitive data about oneself in appropriate circumstances, for example, for the good of public health research or public education.”

Risks might also fall to blood relatives of these individuals who carry similar genomic variants, thereby raising the stakes of privacy concerns in whole genome sequencing compared with most other types of research.”

UPDATE 4: 3/26/13 – Some new stories / links

UPDATE 5: 3/26/13 – Rebecca Skloot on Morning Edition

UPDATE 6: 3/26/13 – Some more stories / discussion

UPDATE 7: 3/26/13 2 PM PST Still waiting for ENCODE to say something about whether they are going to take down their #HeLa data. See for example my Tweet from a few days ago




#UCDavis neurosurgeons conducted experimental surgery w/o IRB approval

Not really sure what to say about this other than that this story should be read by many/all who are interested in medical research and/or UC Davis: 2 UC Davis neurosurgeons accused of experimental surgery are banned from human research – Investigations – The Sacramento Bee.

UPDATE 7/23.  Added a summary: Two UC Davis neurosurgeons were treating terminally ill brain cancer patients with an unapproved, experimental treatment that is referred to as “Probiotic Intracranial Therapy for Malignant Glioma”.  The treatment involved purposefully infecting patients brains with a bacterium Enterobacter aerogenes apparently because of prior anecdotes and case reports that suggested that patients with these brain cancers who also had brain infections might live longer than those with the cancer but without the infection.  According to the article, there was an investigation at UC Davis into the practices of the surgeons.  It was determined by UC Davis that they did not have IRB approval to carry out the treatments and that there were some other issues with the practice going on.  At the conclusion of the investigation UC Davis wrote a letter to the FDA detailing the case and has banned the two neurosurgeons from performing medical research on humans.  Read the article for much more detail and see the link below.

Many interconnected issues in here involving IRB approval, human experimental treatments and informed consent, UC Davis, and even “probiotics”.  Still taking it all in …  Uggh …

Other stories posted in the SacBee at the same time:

See also

UPDATE 7/22/12. Some tidbits to consider
  • The doctors used the bacterium Enterobacter aerogenes for the treatment.  It wear obtained from ATCC and grown by a graduate student at UC Davis.
  • The use of the bacterium for human treatments violated the ATCC MTA.
  • It is unclear from the details here why this bacterial strain/species was selected.  But I assume it is related to the referenced Neurosurgery article (see more below).
  • The hypothesis that purposefully causing an infection may help glioblastoma patients seems to come from the observation that patients with glioblastoma w/ postoperative infections have better survival than those who do not get infections.  This could be due to many many factors jumping to purposefully causing infections with E. aerogenes seems a big big jump.
  • It would be nice to know more about the statement “Early this year, as required by University policy Drs. Muizelaar and Schrot submitted a Record of ~Invention for the bacterial intervention to UCD’s technology transfer office.” in the letter from UCD to the FDA.  Was this just a formality or were the surgeons looking to patent/protect the bacterial treatment method?
  • The Neurosurgery article discussing infection and glioblastoma may be “Long-term Remission of Malignant Brain Tumors after Intracranial Infection: A Report of Four Cases” Neurosurgery: March 1999 – Volume 44 – Issue 3 – pp 636-642.  This reported that some of the patients with infections that seemed to have a longer survival with glioblastoma were infected with E. aerogenes.
    • “In three of the cases described above, Enterobacter aerogenes was recovered from microbial cultures. Whether the presence of Enterobacter aerogenes was coincidental or whether this organism plays an important role in tumor defense is not known and cannot be proven from the cases reported. “
  • See also
UPDATE 3 – some papers on bacterial infections and glioblastoma and other cancers
  • Biocrime or a Passion to Save a Life?.  This pointed me to the article below:
  • A key article of interest: Post-operative infection may influence survival in patients with glioblastoma: simply a myth?: Glioblastoma, infection and survival from 2011. The article casts some doubt on the basis for the treatment used here
    • Citation: De Bonis P, M D AA, M D GL, de Waure C, Mangiola A, Pettorini BL, Pompucci A, Balducci M, Fiorentino A, Lauriola L, Anile C, Maira G. 2011. Post-operative infection may influence survival in patients with glioblastoma: simply a myth?: Glioblastoma, infection and survival. Neurosurgery. 2011 Oct;69(4):864-8; discussion 868-9.
    • “One of the myths that continues to be perpetrated in neurosurgery relates to the observation that a postoperative infection may actually confer a survival advantage in patients with malignant glial tumors”
    • The take-home message of this study, which can be applied to any aspect of neurosurgery, is to do everything possible to prevent a postoperative wound or cavity infection. The association between infection and prolonged survival is not definitive; we acknowledge the considerable difficulties in undertaking this type of study in a retrospective manner in view of the numerous clinical variables. A prospective randomized study on this subject is clearly not possible. Nevertheless, we believe the results of this study are important and can be used as a stimulus for further multicentric studies (to increase the number of patients) or for experimental studies using genetically modified bacteria for the treatment of GBM.
  • Also see The survival impact of postoperative infection in patients with glioblastoma multiform from 2009.
    • In this single-center study, postoperative infection did not confer any survival advantage in patients with glioblastoma multiforme”
    • Available free online here
    • “This study did not show a causal relationship between postoperative infection and prolonged survival in patients with GBM. Although targeted immunotherapy may provide antitumoral effects, simple infection does not appear to do so. Modern aseptic and antiseptic surgical techniques continue to be integral to the care of patients with gliomas.
  • Also see  Cancer J. 2012 Jan-Feb;18(1):59-68. Immunotherapy for the treatment of glioblastoma. Thomas AA, Ernstoff MS, Fadul CE. (though I cannot seem to be able to get a copy ..)

    UPDATE 6: 7/23 10 AM – some info. on UC Davis IRB, Med School, etc

      UPDATE 9: SacBee Editorial calling for Muizelear to step down as Chair
      • The Sac Bee has an editorial today calling for the doctor involved in this issue to step down as chair of the Neurosurgery department.  Some quotes below
      • Experimentation on terminal patients requires a specific set of protections for good reason. People who are, quite literally, on death’s doorstep are extremely vulnerable, and therefore not always able to give informed consent.
      • University officials conceded that “systemic issues” within the medical center may have contributed to errors made and that “additional measures designed to avoid future confusion” have been put in place.”
      • “Curiously, even after it was imposed last fall, the university named Muizelaar to fill its new Julian R. Youmans endowed chair in neurological surgery. The donor specified, university officials explained, that the chair be filled with the head of the department, a fact that begs the question: Why is Muizelaar still chairman of the department?”
      UPDATE 9: some new stories
      UPDATE 11: Muizelaar steps down as chair of department, at least temporarily
      • UC Davis neurosurgeon department chair steps down pending …
        • “One advocate for ethical human subjects research questioned the university’s decision to keep the matter in-house instead of seeking outside review. “The time is long gone for another internal investigation,” said Elizabeth Woeckner, founder and director of Citizens for Responsible Care and Research, or CIRCARE. The nonprofit group works to improve protections for human subjects in research. Woeckner called the doctors’ work on the patients – intentionally infecting them with bacteria restricted to use in lab rats only – as “the worst thing I’ve seen in my 12 years with CIRCARE.””
      UPDATE 12 – September 7, 2012 – some new news stories on Federal investigations
      UPDATE 13: December 11, 2012 – Federal investigation at UC Davis, Resignation of UC Davis Dean of Medicine, more
      UPDATE 16: August 15, 2015
      Well, many things have happened since 2012 – here are some stories to look at

      Conflict of interest and openness

      The New York Times had a long and extensive article on conflicts of interest in medicine. See Times article here. 

      I was pleasantly surprised to see them discuss the concept that open access to data can help correct for bias if it occurs by allowing others to redo analyses.  For example: 

      “Having everyone stand up like a Boy Scout and make a pledge isn’t going to quell suspicion,” said Dr. Donald Klein, an emeritus professor at Columbia, who has consulted with drug makers himself. “The only hope to rule out bias is to have open access to all data that’s produced in studies and know that there are people checking it” who are not on that company’s payroll.

      Unfortunately the Times does not raise the issue of access to the publications themselves.  Clearly having the data is good.  But if nobody can read the papers and they can just read the press releases that come from the papers, we are all doomed.

      UC Davis Med School’s conflict of interest policies among best

      A little late on tis post but still wanted to point out this story in the Davis student newspaper (California Aggie – UC Davis Med School’s conflict of interest policies among best). They report that:

      The American Medical Student Association recently conducted a ranking of medical schools based on their policies regarding free gifts from pharmaceutical companies. UC Davis was one of only seven schools nationwide who received a grade ofA” – meaning the school has a comprehensive policy that restricts pharmaceutical company representatives access to both campuses and academic medical centers.

      Good to see this. I find the layers of real and potential conflicts of interest in medical research in general to be very poorly handled by the community. Not that basic science is immune to this problem either but it seems worse in medical research. For some scathing commentary on conflict of interest in medical research, keep an eye on Steven Salzberg’s blog. Every once in a while he has some juicy stuff to discuss.

      Do you get permission to engineer your microbe?

      Well, lots of researchers manipulate microbes in various ways in the lab. They delete genes. They make mutants They insert genes. Sometimes, they insert antibiotic resistance genes to help with the genetic manipulations they are doing.

      Do researchers always think about the potential risks of what they are doing? Well, probably not. Most of the time that is OK as the risks are negligible. But some of the time, there are real risks to consider. One example of a real risk is the introduction into some pathogen of genes encoding a form of antibiotic resistance not seen normally in that pathogen. If that strain escapes from the lab, it could, in theory, spread into the real world and make treating infections by that pathogen more difficult.

      All Things Considered had a very interesting story on “Making Drug-Resistant Germs In The Lab” about exactly this issue a few days ago where they discussed how one researcher submitted to an NIH oversight panel a request to carry out this type of experiment. It seems as though very few researchers actually submit requests to carry out these experiments, even though many are doing it. NPR also discussed how the CDC reviews requests to manipulate certain really nasty pathogens and that most of the requests have been granted. Unfortunately, I cannot find a transcript for this story to quote, but it is really worth listening to.

      Conflicts of interest, full disclosure, and ethical blogging

      Well, I am sure many have heard stories about scientific research ethics gone awry.  The latest is an article in the New York Times about two Harvard Psychiatry Professors who failed to disclose all of their income from consulting to the University and to the government.  The story they report is pretty icky, with what appear to be clear conflicts of interest not being reported fully.  And this is of course nothing new.  Conflicts of interest and unethical behavior occur of course in every walk of life.  But scientists cringe at it because when it occurs it is really damaging to the whole enterprise.  

      Well, what about bloggers?  Sure there are bloggers railing against conflict of interest and unethical behavior among scientists/MDs (e.g., see Steven Salzberg’s discussion of the recent  “authorship without contribution” controversy).   But that is not what I mean.  What I am interested in here is – what about bloggers disclosing their conflicts of interest?  Is it done?  Is their an ethical code for bloggers?  Should there be?
      So I did some web browsing and there is really a remarkable series of discussions about this on blogs and in other places.  For example:
      These discussions cover every type of “Science Blogging Ethics” including things like how polite one should be, etc.  Personally, I am not sure I want to go so far as to say their should be a code of ethics.  I think the most important thing to think about is “Full Disclosure” of real and possible conflicts of interest.  Sort of like what “real” news entities do when they are reporting on a story they have some connection to (e.g., the New York Times always puts something like “The New York Times is owned by XXX and the company we are reporting on here is also owned by XXX”  
      So from now on I vow to try and do this within my blog (I already do this much of the time when I write about PLoS or my brother but I will try to do it more thoroughly).