New Masterclass: “Papers and Books”

“Navigating numbers” is a series of Masterclass initiated by a team of Charité researchers who think that our students should be able to get more familiar how numbers shape the field of medicine, i.e. both medical practice and medical research. And I get to organize the next in line.

I am very excited to organise the next Masterclass together with J.O. a bright researcher with a focus on health economics. As the full title of the masterclass is “Papers and Books – series 1 – intended effect of treatments”, some health economics knowledge is a must in this journal club style series of meetings.

But what will we exactly do? This Masterclass will focus on reading some papers as well as a book (very surprising), all with a focus on study design and how to do proper research into “intended effect of treatment” . I borrowed this term from one of my former epidemiology teachers, Jan Vandenbroucke, as it helps to denote only a part of the field of medical research with its own idiosyncrasies, yet not limited by study design.

The Masterclass runs for 8 meetings only, and as such not nearly enough to have the students understand all in and outs of proper study design. But that is also not the goal: we want to show the participants how one should go about when the ultimate question is medicine is asked: “should we treat or not?”

If you want to participate, please check out our flyer

Fellow of the European Stroke Organisation

 www.eso-sss-2012.med.unideb.hu

I just got word that I am elected as fellow of the European Stroke Organisation. Well, elected sounds more cool then it really is… I applied myself by sending in an application letter, resume, some form to show my experience in stroke research and two letters of recommendation of two active fellows and that’s that. So what does this mean? Basically, the fellows of the ESO are those who want to put some of their time to good use in name of the ESO, such as being active in one fo the committees. I chose to get active in teaching epidemiology (teaching courses during the ESOC conferences, or in the winter/summer schools, perhaps in the to be founded ESO scientific journal), but how is as of this moment not completely clear yet. Nonetheless, I am glad that I can work with and through this organisation to improve the epidemiological knowledge in the field of stroke.

New publication “Graphical presentation of confounding in directed acyclic graphs”

source: wikimedia.org

A new publication became available, again an ‘educational’. However, this time the topic is new. It is about the application of directed acyclic graphs, a technique widely used in different areas of science. Ranging from computer science, mathematics, psychology, economics and epidemiology, this specific type of graphs has shown to be useful to describe the underlying causal structure of mechanisms of interest. This comes in very handy, since it can help to determine the sources of confounding for a specific epidemiological research question.

But, isn’t that what epidemiologist do all the time? What is new about these graphs, except for the fancy concepts as colliders, edges, and backdoor paths? Well, the idea behind DAGs are not new, there have been diagrams in epidemiology since years, but each epidemiologist has his own specific ways to draw the different relationship between various variables factors. Did you ever got stuck in a discussion about if something is a confounder or not? If you don’t get it resolved by talking, you might want to draw out the your point of view in a diagram, only to see that your colleagues is used to a different way of drawing epidemiological diagrams. DAGs resolve this. There is a clear set on rules that each DAG should comply with and if they do, they provides a clear overview of the sources of confounding and identify the minimal set of variables to account for all confounding present.

So that’s it… DAGs are a nifty method to talk the same idiom while discussing the causal questions you want to resolve. The only thing that you and your colleague now can fight over is the validity of the assumptions made by the DAG you just drew. And that is called good science!

The paper, with first author MMS, appeared in the methodology series of the journal Nephrology Dialysis and Transplantation, can be found here in pdf, and also on my mendeley account.

preconference workshop ‘crash course peer review’ cancelled

I worked together with some partners on a new workshop for young epidemiologist. The title says it all: WEON preconference workshop ‘crash course peer review’.

Unfortunately, we had to cancel the workshop because the number of participants was to low to justify the effort of not only myself, but especially all the other teachers. I think it is a pity that we had to cancel, but by cancelling we still have a fresh start whenever we want to try again in a different format.

Whilst preparing this workshop I noticed that peer review, or a better term would be refereeing, is not popular. It is seen as a task that task up to much time, with too much political consequences and little reward etc. New initiatives like Pubmed commons and other post publication peer review systems are regarded by some as answers to some of these problems. But what is the future of refereeing, when young epidemiologist are not intrinsically motivated to contribute time and effort to the publication process? Only time will tell.

For those who are still interested in this crash course, please contact me via email.

 

Bad Pharma Symposium on the front page of Mare

Mare 2013 11 28 Bad Pharma  - front pageThis week, the Mare decided to run a story on Bad Pharma book by Ben Goldacre and our related symposium. The author, BB did an outstanding job in describing the argument Goldacre brings forward in his book. As you might know, we are organising a symposium for our 300 students that are following our course “academic and scientific training”, because I believe that doctors should learn about their field that they will graduate in once they have graduated. A quote from me in the Mare (in Dutch)

Dokter zijn gaat verder dan alleen het behandelen van één patiënt. Onze beroepsgroep heeft een bijzondere positie in de samenleving; mensen leggen letterlijk hun leven in je handen. Naast je arts-patiëntrelatie heb je ook te maken met de wetenschap, beleidsmakers en de farmaceutische industrie. Aankomende artsen moeten daarvan bewust worden en goed op de hoogte zijn van de ontwikkelingen in hun veld. Dit boek sloeg de spijker op zijn kop.

one little error slipped in… I am not a doctor and therefore it is officially not ‘onze beroepsgroep’ but i think people will grasp the point that I try to make. The complete article can be read here.

Academic and scientific training about to start

After 7 months of preparation the new and improved version of the second year course ‘Academic and Scientific Training’ is about to start. Tomorrow, 300 students will come together for two weeks to learn the how and why of clinical epidemiology. We emphasize on testing new treatments in RCT, and how doctors should critically appraise the articles that describe these studies.

Together with AvHV, JS and others we were able to secure funding to buy 400 copies of the book “Bad Pharma” (click for more background) In order to organise a ‘Bad Pharma Symposium’. In this symposium, all students will read the whole book, do some research on three topics which will be debated in the final debate. This will take a lot of commitment of all students, but what to think of the 40+ Teaching Assistants that we need for this course!

All in all, it’s time to start!

Bad Pharma Symposium

I just got word that we got funding from an external to buy 400 copies of Bad Pharma to use as instruction material in our redesigned course on academic and scientific education. The book touches upon the role of  the pharmaceutical industry in the design, execution, presentation and dissemination of results of clinical trials. The author, Ben Goldacre, identifies several problems and brings forth several solutions. But are these all correct?

We will use this basic question as the basis for a complete symposium on this topic: are the problems identified by Goldacre the real problems, or just cherry picked examples from the past? And are the solutions that he provides real solution that could work? And can we think of any other way to improve the care of our patients in the future?

I had this idea a long time ago when i first read this book. It touches upon a matter that is discussed in the old version of this course for a couple of years. Even more so: during this course students are asked to grade the quality of trials and the subsequent reference to this publication. The results show that the quality is often low, even in high impact journals, and that the references do not always justify the claims made in medical advertisements. These results have been published in several publications and are even cited in the book.

It was quite a hassle to get a ‘normal’ book into the curriculum of our medical center. Most people liked the idea of reading a book and organising a symposium, but a lot of people told me that it was impossible to do so. A “normal” book could not be placed on the mandatory reading list, and just buying electronic or hard copy  versions is just way to expensive. luckily, with help from the Walaeus Library of the LUMC and prof FMH we were able to obtain external funding. And no, its not funded by ‘big pharma’, but a small fund that subsidises small but nice projects that make the world a bit smarter.

New course started today: Scientific education

Today, the course scientific education started. This course, a regular 2nd year course in the LUMC curriculum, runs for three weeks and is organised by AvHV and myself. This is the last year this course will be given in this form, and we are working hard to modify the course to make it fit in the new curriculum. This means that this year we have a opportunity to test some of my our ideas. One of these things is a non compulsory journalclub, in which we’re going to read one article with all students at the same time. I’m curious how may students really would like to train their scientific skills, outside of the curriculum.

Also, we are preparing a new full day interactive assignment and sympium, which is centered around the book Bad Pharma of author Ben Goldacre. I hope to fine some students that are wiling to help me in this development of this part of the new course. Exciting stuff!

– edit 30/5 : the course just finished and 320 students took their exam friday 24th. Although i do like students, I hope I won’t have to see them again for that will mean that they failed the course.

LUMC workshop on scientific integrity

Together with my colleague TdC from the department of geriatrics I am working on a workshop for starting PhD students on the topic of scientific integrity under the working title “On being a scientist: a workshop in scientific integrity”

The LUMC code of scientific integrity, the recent KNAW report of cie. Schuyt and the publication of the National Academy of Science “On being a scientist” will form the backbone of the this workshop (see also the video below of the NAS, with the great quote “scientist should be people too!”). We are still developing the actual content, but this workshop will primarily based on several cases that will be discussed, ranging from cases of clear scientific misconduct to cases of conflicting demands of supervisors. How can you spot these problems in advance, solve or preferably prevent them? What additional measure should be put in place to sustain a critical but workable environment?

I am excited that I can be part of the team that develops this workshop. As I said before, I do not believe that this workshop will prevent all possible scientific misconduct, but I do believe that educating PhD students helps to prevent hem from making honest mistaken. Also, I hope that this course will help to create a critical but positive atmosphere in which science will thrive.

This workshop will be part of the PhD training that the LUMC offers free of charge. The first edition of the this workshop will be held on September 18 2013. Please contact me via email for more information.

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video “on being a scientist” from the NAS

Is science self-cleansing? An article in the “Academische Boekengids” discussing report cie. Schuyt

Earlier I wrote about the “Adviescommissie onderzoeksgegevens in de wetenschap van de KNAW” and their report “Zorgvuldig en integer omgaan met wetenschappelijke onderzoeksgegevens”. This report induced a discussion in the March 2013 edition of the Academische Boekengids .

Three scientist give their vision: Miedema (dean of Medicine at the UMCU) Vandenbroucke (KNAW professor and professor of epidemiology at the LUMC, member of committee Schuyt) and Paul (professor of secularization studies in Groningen). Important to note is that the contradiction between the authors was known beforehand.

Miedema identifies a change in science, especially medical and social science, in which economic and social forces influence science and scientists. These forces have led to a ‘system failure’ of science, leading to shoddy science or in his words ‘post academic science’. Miedema argues that these changes cannot be undone and certain measures need to be taken to correct this system failure. What measures? Miedema points toward Quality Assurance and Quality Control (QA/QC) making a comparison with so called pharmaceutical research embedded within Good Clinical Practice (GCP). This should be done by governments, universities and funding bodies. Interestingly, he leaves scientist out of this list. And what does Miedema think of the report of the committee? He believes the vision of the report is based on the old idea of science where all scientist are directly held accountable by peer pressure, a vision that according to Miedema is not valid in this day and age.

Vandenbroucke points out an error in the argumentation: Miedema targets post academic science. Vandenbroucke agrees that this is a problem, but not the problem discussed by the committee. Their task was to see how data during and after research should be treated in order to keep science workable without to many hiccups and problems. The committee provides some answers but one of the main themes is that scientist should self-regulate, for they are the only experts in this area. This is in contrast to who Miedema who abhors the idea of self-regulation: science is not science anymore, so how can scientist self-regulate with all these strong forces that are incomprehensible to grasp for a simple scientist. Vandenbroucke counteracts Miedema by explaining that his vision of science (science is the search for truth) is not at odds with the problems that arise with post academic science (science is a complex social construct in which forces other than the truth have a big influence). Even more: these two notions can coexist, a concept first noted by Stephen Jay Gould.

Paul tries to reconcile the two previous writers: he agrees with Miedema that in earlier times the scientist was appreciated for his behavior as a person, whereas this view seems to be outdated in this day and age. But Paul also approaches the problem from the other side: the solution of the problems that come with post academic science calls for strong personalities that can counter unwanted forces that trouble science. Paul mentions the work of the science historian which he – ought enough in this context- announces as an ‘honored scientist’ (Dutch: gelauwerde wetenschapper) who published his ‘handsome study’ (Dutch: fraaie studie).

So what are the suggested solutions? Because the authors disagree on the origins of the problem, their solution also differ. Especially Vandenbroucke and Miedema find themselves on first glance diametrically opposed to one other. Vandenbroucke wants to start a discussion bottom up on what it is to be a good scientist, whereas Miedema wants top down QA and QC. These ideas are not new. For example, Jacobus Lubsen also brought this concept in an article in the NRC of December of 2011. Quality control and forensic statistics should increase the detection rate of wrongdoing and should therefore be instituted. I responded to this article with a small letter to the NRC in which I state that complete control is difficult and expensive and often only identifies shoddy and fraudulent science with hindsight. Additionally it will have a preventive effect on bad science, but will it have such an effect on fraud? After all, other fields that have huge governance structures such as banking and accountancy also have their fraud scandals. Even more, the frequency of sloppy science is hardly affected by these measures. A better way to prevent both sloppy and fraudulent science is, I believe, a better training of young scientist. By introducing young scientist to the key concepts of scientific conduct, creating a critical but non-repressive atmosphere, perhaps even in several research groups to prevent tunnel vision of individuals, will lead to an increased informal control and a decrease in sloppy and shoddy science. The committee also mentions this concept and calls this “increasing peer pressure” and puts scientist at the helm of this operation.

It will not surprise you that I agree with Vandenbroucke for the most part. But I also see merit in the argumentation of Miedema. Perhaps I agree with both to some extent because they address two different concepts: science is the quest for knowledge and based on epistemic virtues. Self-regulation by education of young aspiring scientist in a positive but critical atmosphere will increase the quality of research over time. But science is also a social construct and scientist need, besides guidance by peers, governance and regulations for certain scenarios: the cases Stapel and Poldermans as well as the previously discussed book ‘Bad Pharma’ by Ben Goldacre are examples why this might be true. Besides informal peer review and guidance, an extended system of checks and balances, GCP or not, might help to keep colleagues accountable for their work. Science in itself is a system of checks and balances, but this system might be expanded with some form of regulation and standardization with efficacy and efficiency kept in mind. But most of all, now is the time train the young.

– update on 25/3/2013: an interview with both JvdB and FM was published in the NTVG. Together with the editor-in-chief they discuss performing research, obtaining a PhD and publishing your results. click here for the pdf (NTVG website, in Dutch)

 

New article accepted for publication in NTVG

A new article has been accepted in the Nederlands Tijdschrift voor Geneeskunde. The article with the title “patient crossover studies” or “case-crossover studies” is an educational in the Methodology series of the Journal. REJR is the first author of this article and she did a great job on explaining the similarities and differences between this observational study design and the experimental version of this within person comparison. These crossover trials have been discussed by TNB en JGvdB in a previous article in the same series on which i wrote earlier.

Ben Goldacres ‘Bad Pharma’ and research from the LUMC

Ben Goldacre, known from the bestseller Bad Science (book and blog) has a new book, Bad Pharma. Goldacre is always fun to read: science, both the method as the social phenomenon, explained for non-scientist while still interesting for scientist. The same goes for his new title Bad Pharma, where he explains what is right and wrong in the field of clinical trials needed to determine what treatment is best given. Before I am going to review the complete book, perhaps this TED talk will explain it all:

Basically, his point is that for good answers to questions on what treatment is best to save lives, it is pivotal that all the results of all trials are published. This sounds a bit old, since there are databases in which trials should be registered. However, only registering the existence of a trial is not enough: all data should become known to the public. This sounds familiar: this standpoint is off course the same standpoint of the AllTrials.net petition, which is initiated by a.o. Ben Goldacre. For more on AllTrials.net, please see a previous post.

While reading the book of Goldacre it started reading about reasearch done in the Netherlands, where 250 students were looking into the adverts for medication: they checked their quality (was the science OK?) and correct use (does it support the claim?) of the trials in major journals and found that half was of good quality and only half supported the claim. And the nice thing about this research? It was executed at our department as part of one of our  undergraduate courses! All students scored trials and a couple of students were also engaged in the analyses/writing/submission process. The paper from this research, cited by Goldacre, is available from the website of the Netherlands Journal of Medicine.  (pdf, open access) An earlier paper with the same concept but focussed on rheumatoid arthritis medication is also published, also open acces. (pdf)

Masterclass “Noordwijk” covered in the LUMC magazine Cicero

The LUMC magazine “Cicero” covered our Masterclass in Noordwijk. Its a nice description (in Dutch) of two weekend of undergrad-die-hard-epidemiology. One of the students is also interviewed and she concludes:

“Het lukt de docenten om de studenten de hele tijd
te blijven boeien, gedurende twee weekenden van donderdagavond tot zaterdagmiddag. Ik was bang dat ik dat niet zou volhouden. Maar het ging, en het bleef nog leuk ook.”

The text of the article can be found below and here in pdf (cicero 29 jan 2013).  More articles etc can be found on the media page.

Continue reading “Masterclass “Noordwijk” covered in the LUMC magazine Cicero”

ERA-EDTA Istanbul

The 50th edition of the ERA EDTA congress will he be held in Istanbul from the 18th until the 21st in may. Since I mainly work i the field of thrombosis, I have never been to this congress, but I probably will visit it next year: The epidemiological team from the AMC is invite to organise an educational session on clinical epidemiology and they asked me to join their team. The content of this methodological session will resemble the smaller meeting we had last year in Thessaloniki, Greece.

Also, I will also be scoring some abstracts for this meeting: I got an email telling me, or warning me perhaps, to expect up to 80 abstract for me to score. In just a couple of days. Let’s hope that they have clear guidelines to help, otherwise it will be tough nut to crack. Nonetheless, both activities give me some insight in the field of nephrology and will help me to further train my epidemiological teaching skills.

Opzet en interpretatie van mensgebonden onderzoek – slides online

Tomorrow I will teach at the graduate course ‘Design and analysis of clinical research’. My part is to introduce the concept of confounding which i demonstrate through the general  idea of ‘confusing of effects’.  Perhaps a bit ‘oldskool’, but it works as a nice introduction to the concept without a direct confrontation with DAGs etc, especially since it helps to think in ways to prevent / solve this problem in data analyses. What ‘arrow’ in the classic confounding triangle can be removed?

I also go into the concept of ceteris paribus, which is further explored through examples of IV analyses. These examples can be historical (Boylston and inoculation) or recent (mendelian randomisation on CRP and CVD disease).

Slides are present in the presentations section of this website.