Tuesday, 26 June 2018
Preprint publication as karaoke
Doing research, analysing the results, and writing it up is a prolonged and difficult process. Submitting the paper to a journal is an anxious moment. Of course, you hope the editor and reviewers will love it and thank you for giving them the opportunity to read your compelling research. And of course, that never happens. More often you get comments from reviewers pointing out the various inadequacies of your grasp of the literature, your experimental design and your reasoning, leading to further angst as you consider how to reply. But worse than this is silence. You hear nothing. You enquire. You are told that the journal is still seeking reviewers. If you go through that loop a few times, you start to feel like the Jane Austen heroine who, having dressed up in her finery for the ball, spends the evening being ignored by all the men, while other, superficial and gaudy women are snapped up as dance partners.
There have been some downcast tweets in my timeline about papers getting stuck in this kind of journal limbo. When I suggested that it might help to post papers as preprints, several people asked how this worked, so I thought a short account might be useful.
To continue the analogy, a preprint server offers you a more modern world where you can try karaoke. You don't wait to be asked: you grab the microphone and do your thing. I now routinely post all my papers as preprints before submitting them to a journal. It gets the work out there, so even if journals are unduly slow, it can be read and you can get feedback on it.
So how does it work? Pre-prints are electronic articles that are not peer-reviewed. I hope those who know more about the history will be able to comment on this, as I'm hazy on the details, but the idea started with physicists, to whom the thought of waiting around for an editorial process to complete seemed ridiculous. Physicists have been routinely posting their work on arXiv (pronounced 'archive') for years to ensure rapid evaluation and exchange of ideas. They do still publish in journals, which creates a formal version of record, but the arXiv is what most of them read. The success of arXiv led to the development of BioRxiv, and then more recently PsyArXiv and SocArXiv. Some journals also host preprints - I have had good experiences with PeerJ, where you can deposit an article as a preprint, with the option of then updating it to a full submission to the journal if you wish*.
All of these platforms operate some basic quality control. For instance, the BioRxiv website states: 'all articles undergo a basic screening process for offensive and/or non-scientific content and for material that might pose a health or biosecurity risk and are checked for plagiarism'. However, once they have passed screening, articles are deposited immediately without further review.
Contrary to popular opinion, publishing a preprint does not usually conflict with journal policies. You can check the policy of the journal on the Sherpa/ROMEO database: most allow preprints prior to submission.
Sometimes concerns are expressed that if you post a preprint your work might be stolen by someone who'll then publish a journal article before you. In fact, it's quite the opposite. A preprint has a digital object identifier (DOI) and establishes your precedence, so guards against scooping. If you are in a fast-moving field where an evil reviewer will deliberately hold up your paper so they can get in ahead, pre-printing is the answer.
So when should you submit a preprint? I would normally recommend doing this a week or two before submitting to a journal, to allow for the possibility of incorporating feedback into the submitted manuscript, but, given that you will inevitably be asked for revisions by journal reviewers, if you post a preprint immediately before submission you will still have an opportunity to take on board other comments.
So what are the advantages of posting preprints?
1. The most obvious one is that people can access your work in a timely fashion. Preprints are freely available to all: a particularly welcome feature if you work in an area that has implications for clinical practice or policy, where practitioners may not have access to academic journals.
2. There have been cases where authors of a preprint have been invited to submit the work to a journal by an editor. This has never happened to me, but it's nice to know it's a possibility!
3. You can cite a preprint on a job application: it won't count as much as a peer-reviewed publication, but it does make it clear that the work is completed, and your evaluators can read it. This is preferable to just citing work as 'submitted'. Some funders are now also allowing preprints to be cited. https://wellcome.ac.uk/news/we-now-accept-preprints-grant-applications
4. Psychologically, for the author, it can be good to have a sense that the work is 'out there'. You have at least some control over the dissemination of your research, whereas waiting for editors and reviewers is depressing because you just feel powerless.
5. You can draw attention to a preprint on social media and explicitly request feedback. This is particularly helpful if you don't have colleagues to hand who are willing to read your paper. If you put out a request on Twitter, it doesn't mean people will necessarily reply, but you could get useful suggestions for improvement and/or make contact with others interested in your field.
On this final point, it is worth noting that there are several reasons why papers linger in journal limbo: it does not necessarily mean that the journal administration or editor is incompetent (though that can happen!). The best of editors can have a hard job finding reviewers: it's not uncommon to have to invite ten reviewers to find two who agree to review. If your papers is in a niche area then it gets even harder. For these reasons it is crucial to make your title and abstract as clear and interesting as possible: these are the only parts of the paper that potential reviewers will see, and if you are getting a lot of refusals to review, it could be that your abstract is a turn-off. So asking for feedback on a preprint may help you rewrite it in a way that encourages more interest from reviewers.
*Readers: please feel free to add other suggestions while comments are open. (I close comments once the invasion of spammers starts - typically 3-4 weeks after posting).
Saturday, 9 June 2018
Developmental language disorder: the need for a clinically relevant definition
There's been debate over the new terminology for Developmental Language Disorder (DLD) at a meeting (SRCLD) in the USA. I've not got any of the nuance here, but I feel I should make a quick comment on one issue I was specifically asked about, viz:
As background: the field of children's language disorders has been a terminological minefield. The term Specific Language Impairment (SLI) began to be used widely in the 1980s as a diagnosis for children who had problems acquiring language for no apparent reason. One criterion for the diagnosis was that the child's language problems should be out of line with other aspects of development, and hence 'specific', and this was interpreted as requiring normal range nonverbal IQ (nviq).
The term SLI was never adopted by the two main diagnostic systems -WHO's International Classification of Diseases (ICD) or the American Psychiatric Association's Diagnostic and Statistical Manual (DSM), but the notion that IQ should play a part in the diagnosis became prevalent.
In 2016-7 I headed up the CATALISE project with the specific goal of achieving some consensus about the diagnostic criteria and terminology for children's language disorders: the published papers about this are openly available for all to read (see below). The consensus of a group of experts from a range of professions and countries was to reject SLI in favour of the term DLD.
Any child who meets criteria for SLI will meet criteria for DLD: the main difference is that the use of an IQ cutoff is no longer part of the definition. This does not mean that all children with language difficulties are regarded as having DLD: those who meet criteria for intellectual disability, known syndromes or biomedical conditions are treated separately (see these slides for summary).
The tweet seems to suggest we should retain the term SLI, with its IQ cutoff, because it allows us to do neatly controlled research studies. I realise a brief, second-hand tweet about Rice's views may not be a fair portrayal of what she said, but it does emphasise a bone of contention that was thoroughly gnawed in the discussions of the CATALISE panel, namely, what is the purpose of diagnostic terminology? I would argue its primary purpose is clinical, and clinical considerations are not well-served by research criteria.
The traditional approach to selecting groups for research is to find 'pure' cases - quite simply, if you include children who have other problems beyond language (including other neurodevelopmental difficulties) then it is much harder to know how far you are assessing correlates or causes of language problems: things get messy and associations get hard to interpret. The importance of controlling for nonverbal IQ has been particularly emphasised over many years: quite simply, if you compare language-impaired vs comparison (typically-developing, or td) children on a language or cognitive measure, and the language-impaired group has lower nonverbal ability, then it may be that you are looking at a correlate of nonverbal ability rather than language. Restricting consideration to those who meet stringent IQ criteria to equalise the groups is one way of addressing the issue.
However, there are three big problems with this approach:
1. A child's nonverbal IQ can vary from time to time and it will depend on the test that is used. However, although this is problematic, it's not the main reason for dropping IQ cutoffs; the strongest arguments concern validity rather than reliability of an IQ-based approach.
2. The use of IQ-cutoffs ignores the fact that pure cases of language impairment are the exception rather than the rule. In CATALISE we looked at the evidence and concluded that if we were going to insist that you could only get a diagnosis of DLD if you had no developmental problems beyond language, then we'd exclude many children with language problems (see also this old blogpost). If our main purpose is to get a diagnostic system that is clinically workable, it should be applicable to the children who turn up in our clinics - not just a rarefied few who meet research criteria. An analogy can be drawn with medicine: imagine if your doctor identified you with high blood pressure but refused to treat you unless you were in every other regard fit and healthy. That would seem both unfair and ill-judged. Presence of co-occurring conditions might be important for tracking down underlying causes and determining a treatment path, but it's not a reason for excluding someone from receiving services.
3. Even for research purposes, it is not clear that a focus on highly specific disorders makes sense. An underlying assumption, which I remember starting out with, was the idea that the specific cases were in some important sense different from those who had additional problems. Yet, as noted in the CATALISE papers, the evidence for this assumption is missing: nonverbal IQ has very little bearing on a child's clinical profile, response to intervention, or aetiology. For me, what really knocked my belief in the reality of SLI as a category was doing twin studies: typically, I'd find that identical twins were very similar in their language abilities, but they sometimes differed in nonverbal ability, to the extent that one met criteria for SLI and the other did not. Researchers who treat SLI as a distinct category are at risk of doing research that has no application to the real world.
There is nothing to stop researchers focusing on 'pure' cases of language disorder to answer research questions of theoretical interest, such as questions about the modularity of language. This kind of research uses children with a language disorder as a kind of 'natural experiment' that may inform our understanding of broader issues. It is, however, important not to confuse such research with work whose goal is to discover clinically relevant information.
If practitioners let the theoretical interests of researchers dictate their diagnostic criteria, then they are doing a huge disservice to the many children who end up in a no-man's-land, without either diagnosis or access to intervention.
References
Bishop, D. V. M. (2017). Why is it so hard to reach agreement on terminology? The case of developmental language disorder (DLD). International Journal of Language & Communication Disorders, 52(6), 671-680. doi:10.1111/1460-6984.12335
Bishop, D. V. M., Snowling, M. J., Thompson, P. A., Greenhalgh, T., & CATALISE Consortium. (2016). CATALISE: a multinational and multidisciplinary Delphi consensus study. Identifying language impairments in children. PLOS One, 11(7), e0158753. doi:10.1371/journal.pone.0158753
Bishop, D. V. M., Snowling, M. J., Thompson, P. A., Greenhalgh, T., & CATALISE Consortium. (2017). Phase 2 of CATALISE: a multinational and multidisciplinary Delphi consensus study of problems with language development: Terminology. Journal of Child Psychology and Psychiatry, 58(10), 1068-1080. doi:10.1111/jcpp.12721
As background: the field of children's language disorders has been a terminological minefield. The term Specific Language Impairment (SLI) began to be used widely in the 1980s as a diagnosis for children who had problems acquiring language for no apparent reason. One criterion for the diagnosis was that the child's language problems should be out of line with other aspects of development, and hence 'specific', and this was interpreted as requiring normal range nonverbal IQ (nviq).
The term SLI was never adopted by the two main diagnostic systems -WHO's International Classification of Diseases (ICD) or the American Psychiatric Association's Diagnostic and Statistical Manual (DSM), but the notion that IQ should play a part in the diagnosis became prevalent.
In 2016-7 I headed up the CATALISE project with the specific goal of achieving some consensus about the diagnostic criteria and terminology for children's language disorders: the published papers about this are openly available for all to read (see below). The consensus of a group of experts from a range of professions and countries was to reject SLI in favour of the term DLD.
Any child who meets criteria for SLI will meet criteria for DLD: the main difference is that the use of an IQ cutoff is no longer part of the definition. This does not mean that all children with language difficulties are regarded as having DLD: those who meet criteria for intellectual disability, known syndromes or biomedical conditions are treated separately (see these slides for summary).
The tweet seems to suggest we should retain the term SLI, with its IQ cutoff, because it allows us to do neatly controlled research studies. I realise a brief, second-hand tweet about Rice's views may not be a fair portrayal of what she said, but it does emphasise a bone of contention that was thoroughly gnawed in the discussions of the CATALISE panel, namely, what is the purpose of diagnostic terminology? I would argue its primary purpose is clinical, and clinical considerations are not well-served by research criteria.
The traditional approach to selecting groups for research is to find 'pure' cases - quite simply, if you include children who have other problems beyond language (including other neurodevelopmental difficulties) then it is much harder to know how far you are assessing correlates or causes of language problems: things get messy and associations get hard to interpret. The importance of controlling for nonverbal IQ has been particularly emphasised over many years: quite simply, if you compare language-impaired vs comparison (typically-developing, or td) children on a language or cognitive measure, and the language-impaired group has lower nonverbal ability, then it may be that you are looking at a correlate of nonverbal ability rather than language. Restricting consideration to those who meet stringent IQ criteria to equalise the groups is one way of addressing the issue.
However, there are three big problems with this approach:
1. A child's nonverbal IQ can vary from time to time and it will depend on the test that is used. However, although this is problematic, it's not the main reason for dropping IQ cutoffs; the strongest arguments concern validity rather than reliability of an IQ-based approach.
2. The use of IQ-cutoffs ignores the fact that pure cases of language impairment are the exception rather than the rule. In CATALISE we looked at the evidence and concluded that if we were going to insist that you could only get a diagnosis of DLD if you had no developmental problems beyond language, then we'd exclude many children with language problems (see also this old blogpost). If our main purpose is to get a diagnostic system that is clinically workable, it should be applicable to the children who turn up in our clinics - not just a rarefied few who meet research criteria. An analogy can be drawn with medicine: imagine if your doctor identified you with high blood pressure but refused to treat you unless you were in every other regard fit and healthy. That would seem both unfair and ill-judged. Presence of co-occurring conditions might be important for tracking down underlying causes and determining a treatment path, but it's not a reason for excluding someone from receiving services.
3. Even for research purposes, it is not clear that a focus on highly specific disorders makes sense. An underlying assumption, which I remember starting out with, was the idea that the specific cases were in some important sense different from those who had additional problems. Yet, as noted in the CATALISE papers, the evidence for this assumption is missing: nonverbal IQ has very little bearing on a child's clinical profile, response to intervention, or aetiology. For me, what really knocked my belief in the reality of SLI as a category was doing twin studies: typically, I'd find that identical twins were very similar in their language abilities, but they sometimes differed in nonverbal ability, to the extent that one met criteria for SLI and the other did not. Researchers who treat SLI as a distinct category are at risk of doing research that has no application to the real world.
There is nothing to stop researchers focusing on 'pure' cases of language disorder to answer research questions of theoretical interest, such as questions about the modularity of language. This kind of research uses children with a language disorder as a kind of 'natural experiment' that may inform our understanding of broader issues. It is, however, important not to confuse such research with work whose goal is to discover clinically relevant information.
If practitioners let the theoretical interests of researchers dictate their diagnostic criteria, then they are doing a huge disservice to the many children who end up in a no-man's-land, without either diagnosis or access to intervention.
References
Bishop, D. V. M. (2017). Why is it so hard to reach agreement on terminology? The case of developmental language disorder (DLD). International Journal of Language & Communication Disorders, 52(6), 671-680. doi:10.1111/1460-6984.12335
Bishop, D. V. M., Snowling, M. J., Thompson, P. A., Greenhalgh, T., & CATALISE Consortium. (2016). CATALISE: a multinational and multidisciplinary Delphi consensus study. Identifying language impairments in children. PLOS One, 11(7), e0158753. doi:10.1371/journal.pone.0158753
Bishop, D. V. M., Snowling, M. J., Thompson, P. A., Greenhalgh, T., & CATALISE Consortium. (2017). Phase 2 of CATALISE: a multinational and multidisciplinary Delphi consensus study of problems with language development: Terminology. Journal of Child Psychology and Psychiatry, 58(10), 1068-1080. doi:10.1111/jcpp.12721
Labels:
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Sunday, 27 May 2018
Sowing seeds of doubt: how Gilbert et al’s critique of the reproducibility project has played out
In
Merchants of Doubt, Eric Conway and Naomi Oreskes describe how raising
doubt can be used as an effective weapon against inconvenient science. On
topics such as the effects of tobacco on health, climate change and causes of
acid rain, it has been possible to delay or curb action to tackle problems by
simply emphasising the lack of scientific consensus. This is always an option,
because science is characterised by uncertainty, and indeed, we move forward by
challenging one another’s findings: only a dead science would have no
disagreements. But those raising concerns wield a two-edged sword: spurious and discredited criticisms can disrupt scientific progress,
especially if the arguments are complex and technical: people will be left with
a sense that they cannot trust the findings, even if they don’t fully
understand the matters under debate.
The parallels with Merchants of Doubt occurred to me as I
re-read the critique
by Gilbert et al of the classic paper by the Open Science Collaboration (OSC)
on ‘Estimating
the reproducibility of psychological science’. I was prompted to do so
because we were discussing the OSC paper in a journal club* and inevitably the
question arose as to whether we needed to worry about reproducibility, in the
light of the remarkable claim by Gilbert et al: ‘We show
that OSC's article contains three major statistical errors and, when corrected,
provides no evidence of a replication crisis. Indeed, the evidence is also
consistent with the opposite conclusion -- that the reproducibility of
psychological science is quite high and, in fact, statistically
indistinguishable from 100%.’
The Gilbert et al critique has, in turn, been the subject of
considerable criticism, as well as a response by a
subset of the OSC group. I summarise the main points of contention in Table
1: at times they seem to be making a defeatist argument that we don’t need to
worry because replication in psychology is bound to be poor: something I
have disputed.
But my main focus in this post is simply to consider the
impact of the critique on the reproducibility debate by looking at citations of
the original article and the critique. A quick check on Web of Science found
797 citations of the OSC paper, 67 citations of Gilbert et al, and 33 citations
of the response by Anderson et al.
The next thing I did, admittedly in a very informal fashion,
was to download the details of the articles citing Gilbert et al and code them
according to the content of what they said, as either supporting Gilbert et
al’s view, rejecting the criticism, or being neutral. I discovered I needed a
fourth category for papers where the citation seemed wrong or so vague as to be unclassifiable. I discarded any papers where the relevant information could
not be readily accessed – I can access most journals via Oxford University but
a few were behind paywalls, others were not in English, or did not appear to
cite Gilbert et al. This left 44 citing papers that focused on the commentary
on the OSC study. Nine of these were supportive of Gilbert et al, two noted
problems with their analysis, but 33 were categorised as ‘neutral’, because the
citation read something like this:
“Because of the
current replicability crisis in psychological science (e.g., Open Science
Collaboration, 2015; but see Gilbert, King, Pettigrew, & Wilson, 2016)….”
The strong impression was that the authors of these papers lacked
either the appetite or the ability to engage with the detailed arguments in the
critique, but had a sense that there was a debate and felt that they should
flag this up. That’s when I started to think about Merchants of Doubt: whether intentionally or not, Gilbert et al had created an atmosphere of uncertainty to suggest there is no consensus on whether or not psychology has a reproducibility problem - people are left thinking that it's all very complicated and depends on arguments that are only of interest to statisticians. This makes it easier for those who are reluctant to take action to deal with the issue.
Fortunately, it looks as if Gilbert et al’s critique has
been less successful than might have been expected, given the eminence of the
authors. This may in part be because the arguments in favour of change are
founded not just on demonstrations such as the OSC project, but also on logical
analyses of statistical practices and publication biases that have been known
about for years (see slides 15-20 of my presentation here). Furthermore, as evidenced in the footnotes to Table 1, social
media allows a rapid evaluation of claims and counter-claims that hitherto was
not possible when debate was restricted to and controlled by journals. The publication this
week of three more big replication studies
just heaps on further empirical evidence that we have a problem that
needs addressing. Those who are saying ‘nothing to see here, move along’ cannot
retain any credibility.
Table 1
|
Criticism
|
Rejoinder
|
|
‘many of OSC’s replication studies drew their samples from
different populations than the original studies did’
|
·
‘Many’ implies the majority. No attempt to
quantify – just gives examples
·
Did not show that this feature affected
replication rate
|
|
‘many of OSC’s replication studies used procedures that
differed from the original study’s procedures in substantial ways.’
|
·
‘Many’ implies the majority. No attempt to
quantify – just gives examples
·
OSC showed that this did not affect
replication rate
·
Most striking example used by Gilbert et al is
given detailed explanation by Nosek (1)
|
|
‘How many of their replication studies should we expect to
have failed by chance alone? Making this estimate requires having data from
multiple replications of the same original study.’
Used data from pairwise comparisons of studies from the
Many Labs project to argue a low rate of agreement is to be expected.
|
·
Ignores publication bias impact on original
studies (2, 3)
·
G et al misinterpret confidence intervals (3,
4)
·
G et al fail to take sample size/power into
account, though this is crucial determinant of confidence interval (3, 4)
·
‘Gilbert
et al.’s focus on the CI measure of reproducibility neither addresses nor can
account for the facts that the OSC2015 replication effect sizes were about
half the size of the original studies on average, and 83% of replications
elicited smaller effect sizes than the original studies.’ (2)
|
|
Results depended on whether original authors endorsed the
protocol for the replication: ‘This strongly suggests that the infidelities
did not just introduce random error but instead biased the replication
studies toward failure.
|
·
Use of term ‘the infidelities’ assumes the only
reason for lack of endorsement is departure from original protocol. (2)
·
Lack of endorsement included non-response from
original authors (3)
|
(1)
Nosek: https://retractionwatch.com/2016/03/07/lets-not-mischaracterize-replication-studies-authors/
(2)
Anderson et al: http://science.sciencemag.org/content/351/6277/1037.3
(3)
Srivastava:
https://thehardestscience.com/2016/03/03/evaluating-a-new-critique-of-the-reproducibility-project/
References
Anderson, C. J., Bahnik, S., Barnett-Cowan, M., & et al. (2016).
Response to Comment on "Estimating the reproducibility of psychological
science". Science, 351(6277).
Gilbert, D. T., King, G., Pettigrew, S., & Wilson, T. D. (2016).
Comment on "Estimating the reproducibility of psychological science".
Science, 351(6277).
Open Science Collaboration. (2015). Estimating the reproducibility
of psychological science. Nature, 349(6251). doi:10.1126/science.aac4716
*Thanks to the enthusiastic efforts of some of our grad
students, and the support of Reproducible
Research Oxford, we’ve had a series of Reproducibilitea
journal clubs in our department this term.
I can recommend this as a great – and relatively cheap and easy - way of
raising awareness of issues around reproducibility in a department: something
that is sorely needed if a recent Twitter survey by Dan Lakens
is anything to go by.
Sunday, 13 May 2018
How to survive on Twitter – a simple rule to reduce stress
In recent weeks, I’ve seen tweets from a handful of people I
follow saying they are thinking of giving up Twitter because it has become so
negative. Of course they are entitled to do so, and they may find that it frees
up time and mental space that could be better used for other things. The
problem, though, is that I detect a sense of regret. And this is appropriate because Twitter, used judiciously,
has great potential for good.
For me as an academic, the benefits include:
·
Finding out about latest papers and other
developments relevant to my work
·
Discovering new people with interesting points
of view – often these aren’t eminent or well-known and I’d never have come
across them if I hadn’t been on social media
·
Being able to ask for advice from experts –
sometimes getting a remarkably quick and relevant response
·
Being able to interact with non-academics who
are interested in the same stuff as me
·
Getting a much better sense of the diversity of
views in the broader community about topics I take for granted – this often
influences how I go about public engagement
·
Having fun – there are lots of witty people who brighten
my day with their tweets
The bad side, of course, is that some people say things on
Twitter that they would not dream of saying to your face. They can be rude,
abusive, and cruel, and sometimes mind-bogglingly impervious to reason. We now
know that some of them are not even real people – they are just bots set up by
those who want to sow discord among those with different political views. So
how do we deal with that?
Well, I have a pretty simple rule that works for me, which
is that if I find someone rude, obnoxious, irritating or tedious, I mute them.
Muting differs from blocking in that the person doesn’t know they are muted. So
they may continue hurling abuse or provocations at you, unaware that they are
now screaming into the void.
A few years ago, when I first got into a situation where I
was attacked by a group of unpleasant alt-right people (who I now realise were
probably mostly bots), it didn’t feel right to ignore them, for three reasons:
·
First, they were publicly maligning me, and I
felt I should defend myself.
·
Second, we’ve been told to beware the Twitter
bubble. If we only interact on social media with those who are like-minded: it
can create a totally false impression of what the world is like.
·
Third, walking away from an argument is not a
thing a good academic does: we are trained experts in reasoned debate, and our
whole instinct is to engage with those who disagree with us, examine what they
say and make a counterargument.
But I soon learned that some people on social media don’t
play by the rules of academic engagement. They are not sincere in their desire
to discuss topics: they have a viewpoint that nothing will change, and they
will use any method they can find to discredit an opponent. This includes ad
hominem attacks, lying and wilful misrepresentation of what you say. It's not cowardly to avoid these people: it's just a sensible reaction. So I now just mute anyone where I get a
whiff of such behaviour – directed either towards me or anyone else.
The thing is, social media is so different from normal
face-to-face interaction, that it needs different rules. Just imagine if you
were sitting with friends at the pub, having a chat, and someone barged in and
started shouting at you aggressively. Or someone sat down next to you,
uninvited, and proceeded to drone on about a very boring topic, impervious to
the impact they are having. People may have different ways of extricating
themselves from these situations, but one thing you can be sure of: when you
next go to the pub, you would not seek these individuals out and try to engage them
in discussion.
So my rule boils down to this: Ask yourself, if I was
talking to this person in the pub, would I want to prolong the interaction? Or,
if there was a button that I could press to make them disappear, would I use
it? Well, on social media, there is such
a button, and I recommend taking advantage of it.*
*I should make it clear that there are situations
when a person is subject to such a volume of abuse that this isn’t going to be
effective. Avoidance of Twitter for a while may be the only sensible option in
such cases. My advice is intended for those who aren’t the centre of a
vitriolic campaign, but who are turned off Twitter because of the stress it causes to observe or participate in hostile Twitter exchanges.
Wednesday, 9 May 2018
My response to the EPA's 'Strengthening Transparency in Regulatory Science'
Incredible things have happened at the US Environmental Protection Agency since Donald Trump was elected. The agency is responsible for creating standards and laws that promote the health of individuals and the environment. During previous administrations it has overseen laws concerned with controlling pollution and regulating carbon emissions. Now, under Administrator Scott Pruitt, the voice of industry and climate scepticism is in the ascendant.
A new rule that purports to 'Strengthen Transparency in Regulatory Science' has now been proposed - ironically, at a time when the EPA is being accused of a culture of secrecy regarding its own inner workings. Anyone can comment on the rule here: I have done so, but my comment appears to be in moderation, so I am posting it here.
A new rule that purports to 'Strengthen Transparency in Regulatory Science' has now been proposed - ironically, at a time when the EPA is being accused of a culture of secrecy regarding its own inner workings. Anyone can comment on the rule here: I have done so, but my comment appears to be in moderation, so I am posting it here.
Dear Mr Pruitt
re: Regulatory
Science- Docket ID No. EPA-HQ-OA-2018-0259
The proposed rule,
‘Strengthening transparency in regulatory science’ brings together two strands
of contemporary scientific activity. On the one hand, there is a trend to make
policy more evidence-based and transparent. On the other hand, there has, over the
past decade, been growing awareness of problems with how science is being done,
leading to research that is not always reproducible (the same results achieved
by re-analysis of the data) or replicable (similar results when an experiment
is repeated). The proposed rule by the Environmental Protection Agency (EPA)
brings these two strands together by proposing that policy should only be based
on research that has openly available public data. While this may on the
surface sound like a progressive way of integrating these two strands, it rests
on an over-simplified view of how science works and has considerable potential
for doing harm.
I am writing in a
personal capacity, as someone at the forefront of moves to improve
reproducibility and replication of science in the UK. I chaired a symposium at
the Academy of Medical Sciences on this topic in 2015; this was jointly
organised with UK major funders: Wellcome Trust, Medical Research Council and
Biotechnology and Biological Science Research Council (https://acmedsci.ac.uk/policy/policy-projects/reproducibility-and-reliability-of-biomedical-research).
I am involved in training early career researchers in methods to improve
reproducibility, and I am a co-author of Munafò, M. R et al (2017). A manifesto for reproducible science.
Nature Human Behavior, 1(1: 0021). doi:10.1038/s41562-016-0021. I would welcome
any move by the US Government that would strengthen research by encouraging
adoption of methods to improve science, including making analysis scripts and data
open when this is not in conflict with legal/ethical issues. Unfortunately,
this proposal will not do that. Instead, it will weaken science by drawing a
line in the sand that effectively disregards scientific discoveries prior to
the first part of the 21st century when the importance of open data started to
be increasingly recognised.
The proposal ignores a
key point about how scientific research works: the time scale. Most studies
that would be relevant to EPA take years to do, and even longer to filter
through to affect policy. Consequences for people and the planet that are
relevant to environmental protection are often not immediately obvious: if they
were, we would not need research. Recognition, for instance, of the dangers of
asbestos, took years because the impacts on health were not immediate. Work
demonstrating the connection occurred many years ago and I doubt that the data
are anywhere openly available, yet the EPA’s proposed rule would imply that it
could be disregarded. Similarly, I doubt there is open data demonstrating the
impact of lead in paint or exhaust fumes, or of pesticides such as DDT: does
this mean that manufacturers would be free to reintroduce these?
A second point is that
scientific advances never depend on a single study: having open scripts and
data is one way of improving our ability to check findings, but it is a
relatively recent development, and it is certainly not the only way to validate
science. The growth of knowledge has always depended on converging evidence
from different sources, replications by different scientists and theoretical
understanding of mechanisms. Scientific facts become established when the
evidence is overwhelming. The EPA proposal would throw out the mass of
accumulated scientific evidence from the past, when open practices were not
customary – and indeed often not practical before computers for big data were
available.
Contemporary
scientific research is far from perfect, but the solution is not to ignore it,
but to take steps to improve it and to educate policy-makers in how to identify
strong science; government needs advisors who have scientific expertise and no
conflict of interest, who can integrate existing evidence with policy
implications. The ‘Strengthening Transparency’ proposal is short-sighted and
dangerous and appears to have been developed by people with little
understanding of science. It puts citizens at risk of significant damage – both
to health and prosperity - and it will
make the US look scientifically illiterate to the rest of the world.
Yours sincerely
D. V. M. Bishop
FMedSci, FBA, FRS
Thursday, 3 May 2018
Power, responsibility and role models in academia
Last week, Robert
J. Sternberg resigned as Editor of Perspectives on Psychological Science after
a series of criticisms of his behaviour on social media. I first became aware
of this issue when Bobbie Spellman wrote a blogpost
explaining why she was not renewing her membership of the Association for
Psychological Science, noting concerns about Sternberg’s editorial bias and high
rate of self-citation, among other issues.
Then a grad student at the University of Leicester, Brendan
O’Connor, noted that Sternberg not only had a tendency to cite his own work; he
also recycled large portions of written text in his publications. Nick Brown
publicised some striking examples on his
blog, and Retraction Watch subsequently published an interview
with O’Connor explaining the origins of the story.
In discussing
his resignation, Sternberg admitted to ‘lapses in judgement and mistakes’
but also reprimanded those who had outed him for putting their concerns online,
rather than contacting him directly. A loyal colleague, James C. Kaufman, then came
to his defence, tweeting:
The term ‘witch-hunt’ is routinely trotted out whenever a
senior person is criticised. (Indeed, it has become one of Donald Trump’s
favourite terms to describe attempts to call him out for various misbehaviours).
It implies that those who are protesting at wrongdoing are self-important
people who are trying to gain attention by whipping up a sense of moral panic about
relatively trivial matters.
I find this both irritating and symptomatic of a deep problem
in academic life. I do not regard Sternberg’s transgressions as particularly
serious: He used his ready access to a publishing platform for self-promotion
and self-plagiarism, was discovered, and resigned his editorial position with a
rather grumbly semi-apology. If that was all there was to it, I would agree that everyone should move on.
The problem is with the attitude of senior people such as
Kaufman. A key point is missed by those who want to minimise Sternberg’s
misbehaviour: He is one of the most successful psychologists in the world, and
so to the next generation, he is a living embodiment of what you need to do to
become a leader in the field. So
early-career scientists will look at him and conclude that to get to the top
you need to bend the rules.
In terms of abuse of editorial power, Sternberg’s behaviour
is relatively tame. Consider the case of Johnny Matson, Jeff Sigafoos, Giuliano
Lancioni and Mark O’Reilly, who formed a coterie of editors and editorial board
members who enhanced their publications and citations by ditching usual
practices such as peer review when handling one another’s papers. I documented
the evidence for this back in 2015, and there appear to have been no
consequences for any of these individuals. You might think it isn’t so important
if a load of dodgy papers make it into a few journals, but in this case, there
was potential for damage beyond academia: the subject matter concerned
developmental disorders, and methods of assessment and intervention were given unjustified
credibility by being published in journals that were thought to be
peer-reviewed. In addition, the corrosive influence on the next generation of psychologists
was all too evident: When I first wrote about this, I was contacted by several
early-career people who had worked with the dodgy editors: they confirmed that
they were encouraged to adopt similar practices if they wanted to get ahead.
When we turn to abuse of personal power, there have been
instances in academia that are much, much worse than editorial misdemeanours –
clearly documented cases of senior academics acting as sexual predators on
junior staff – see, for instance, here
and here.
With the #MeToo campaign (another ‘witch-hunt’),
things are starting to change, but the recurring theme is that if you are sufficiently
powerful you can get away with almost anything.
Institutions that hire top academics seem desperate to cling
on to them because they bring in grants and fame. Of course, accusations need to be fully
investigated in a fair and impartial fashion, but in matters such as editorial
transgressions, the evidence is there for all to see, and a prompt response is
required.
The problem with the academic hierarchy is that at the top there
is a great deal of power and precious little responsibility. Those who make it
to positions of authority should uphold high professional standards and act as academic
role models. At a time when many early-career researchers are complaining
that their PIs are encouraging them to adopt bad scientific practices,
it’s all the more important that we don’t send the message that you need to act
selfishly and cut corners in order to succeed.
I don’t want to see Sternberg vilified, but I do think the
onus is now on the academic establishment to follow Bobbie Spellman’s lead and state
publicly that his behaviour fell below what we would expect from an academic
role model – rather than sweeping it under the carpet or, even worse, portraying
him as a victim.
Saturday, 7 April 2018
Should research funding be allocated at random?
Earlier this week, a group of early-career scientists had an
opportunity to quiz Jim Smith, Director of Science at the Wellcome Trust. The
ECRs were attending a course on Advanced Methods for Reproducible Science that
I ran with Chris Chambers and Marcus Munafo, and Jim kindly agreed to come
along for an after-dinner session which started in a lecture room and ended in
the bar.
Among other things, he was asked about the demand for
small-scale funding. In some areas of science, a grant of £20-30K could be very
useful in enabling a scientist to employ an assistant to gather data, or to buy
a key piece of equipment. Jim pointed out that from a funder’s perspective,
small grants are not an attractive proposition, because the costs of
administering them (finding reviewers, running grant panels, etc.) are high
relative to the benefits they achieve. And it’s likely that there will be far
more applicants for small grants.
This made me wonder whether we might retain the benefits of
small grants by dispensing with the bureaucracy. A committee would have to
scrutinise proposals to make sure that the proposal met the funder’s remit, and
were of high methodological quality; provided that were so, then the proposal could
be entered into a pool, with winners selected at random.
Implicit in this proposal is the idea that it isn’t possible
to rank applications reliably. If a lottery approach meant we ended up funding
weak research and denying funds to excellent project, this would clearly be a
bad thing. But research rankings by committee and/or peer review is notoriously
unreliable, and it is hard to compare proposals that span a range of
disciplines. Many people feel that funding is already a lottery, albeit an
unintentional one, because the same grant that succeeds in one round may be
rejected in the next. Interviews are problematic because they mean that a major
decision – fund or not – is decided on the basis of a short sample of a
candidate’s behaviour, and that people with great proposals but poor social
skills may be turned down in favour of glib individuals who can sell themselves
more effectively.
I thought it would be interesting to float this idea in a
Twitter poll. I anticipated that enthusiasm
for the lottery approach might be higher among those who had been unsuccessful
in getting funding, but in fact, the final result was pretty similar, regardless
of funding status of the respondent: most approved of a lottery approach, with
66% in favour and 34% against.
As is often the way with Twitter, the poll encouraged people
to point me to an existing literature I had not been aware of. In particular, last
year, Mark Humphries (@markdhumphries) made a
compelling argument for randomness in funding allocations, focusing on the
expense and unreliability of current peer review systems. Hilda Bastian
and others pointed me to
work by Shahar Avin , who has done a detailed scholarly analysis of policy
implications for random funding – in the course of which he mentions three
funding systems where this has been tried. In
another manuscript, Avin presented a computer simulation to compare
explicit random allocation with peer review. The code is openly
available, and the results from the scenarios modelled by Avin are provocative
in supporting the case for including an element of randomness in funding. (Readers
may also be interested in this simulation of the
effect of luck on a meritocracy, which is not specific to research funding
but has some relevance.) Others pointed to even more radical proposals, such as
collective
allocation of science funding, giving
all researchers a limited amount of funding, or yoking
risk to reward.
Having considered these sources and a range of additional comments
on the proposal, I think it does look as if it would be worth a funder such as
Wellcome Trust doing a trial of random allocation of funding for proposals
meeting a quality criterion. As noted by Dylan Wiliam,
the key question is whether peer review does indeed select the best proposals.
To test this, those who applied for Seed Funding could be randomly directed to
either stream A, where proposals undergo conventional evaluation by committee,
or stream B, where the committee engages in a relatively light touch process to
decide whether to enter the proposal into a lottery, which then decides its
fate. Streams A and B could each have the same budget, and their outcomes could
be compared a few years later.
One reason I’d recommend this approach specifically for Seed
Funding is because of the disproportionate administrative burden for small
grants. There would, in principle, be no reason for not extending the idea to
larger grants, but I suspect that the more money is at stake, the greater will
be the reluctance to include an explicit element of chance in the funding
decision. And, as Shahar Avin noted, very expensive projects need long-term
support, which makes a lottery approach unsuitable.
Some of those responding to the poll noted potential
drawbacks. Hazel
Phillips suggested that random assignment would make it harder to include
strategic concerns, such as career stage or importance of topic. But if the
funder had particular priorities of this kind, they could create a separate pool
for a subset of proposals that met additional criteria and that would be given
a higher chance of funding. Another concern was gaming by institutions or
individuals submitting numerous proposals in scattergun fashion. Again, I don’t
see this as a serious objection, as (a) use of an initial quality triage would
weed out proposals that were poorly motivated and (b) applicants could be
limited to one proposal per round. Most of the other comments that were
critical expressed concerns about the initial triage: how would the threshold
for entry into the pool be set? A triage
stage may look as if one is just pushing back the decision-making problem to an
earlier step, but in practice, it would be feasible to develop transparent
criteria for determining which proposals didn’t get into the pool: some have methodological
limitations which mean they couldn’t give a coherent answer to the question
they pose; some research questions are ill-formed; others have already been
answered adequately - this
blogpost by Paul Glasziou and Iain Chalmers makes a good start in
identifying characteristics of research proposals that should not be considered
for funding.
My view is that there are advantages for the lottery
approach over and above the resource issues. First, Avin’s analysis concludes
that reliance on peer review leads to a bias against risk-taking, which can
mean that novelty and creativity are discouraged. Second, once a proposal was
in the pool, there would be no scope for bias against researchers in terms of
gender or race – something that can be a particular concern when interviews are
used to assess. Third, the impact on the science community is also worth
considering. Far less grief would be engendered by a grant rejection if you
knew it was that you were unlucky, rather than that you were judged to be wanting.
Furthermore, as noted by Marina Papoutsi,
some institutions evaluate their staff in terms of how much grant income they
bring in – a process that ignores the strong element of chance that already
affects funding decisions. A lottery approach, where the randomness is
explicit, would put paid to such practices.
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