Archive for the ‘science’ Category
Science is broken; let’s fix it. This has been my mantra for some years now, and today we are launching an initiative aimed squarely at one of science’s biggest problems. The problem is called publication bias or the file-drawer problem and it’s resulted in what some have called a replicability crisis.
When researchers do a study and get negative or inconclusive results, those results usually end up in file drawers rather than published. When this is true for studies attempting to replicate already-published findings, we end up with a replicability crisis where people don’t know which published findings can be trusted.
To address the problem, Dan Simons and I are introducing a new article format at the journal Perspectives on Psychological Science (PoPS). The new article format is called Registered Replication Reports (RRR). The process will begin with a psychological scientist interested in replicating an already-published finding. They will explain to we editors why they think replicating the study would be worthwhile (perhaps it has been widely influential but had few or no published replications). If we agree with them, they will be invited to submit a methods section and analysis plan and submit it to we editors. The submission will be sent to reviewers, preferably the authors of the original article that was proposed to be replicated. These reviewers will be asked to help the replicating authors ensure their method is nearly identical to the original study. The submission will at that point be accepted or rejected, and the authors will be told to report back when the data comes in. The methods will also be made public and other laboratories will be invited to join the replication attempt. All the results will be posted in the end, with a meta-analytic estimate of the effect size combining all the data sets (including the original study’s data if it is available). The Open Science Framework website will be used to post some of this. The press release is here, and the details can be found at the PoPS website.
Professor Daniel J. Simons (University of Illlinois) and I are co-editors for the RRRs. The chief editor of Perspectives on Psychological Science is Barbara A. Spellman (University of Virginia), and leadership and staff at the Association for Psychological Science, especially Eric Eich and Aime Ballard, have also played an important role (see their press release).
Three features make RRRs very different from the usual way that science gets published:
1. Preregistration of replication study design and analysis plan and statistics to be conducted BEFORE the data is collected.
- Normally researchers have a disincentive to do replication studies because they usually are difficult to publish. Here we circumvent the usual obstacles to replications by giving researchers a guarantee (provided they meet the conditions agreed during the review process) that their replication will be published, before they do the study.
- There will be no experimenter degrees of freedom to analyse the data in multiple ways until a significant but likely spurious result is found. This is particularly important for complex designs or multiple outcome variables, where those degrees of freedom allow one to always achieve a significant result. Not here.
2. Study is sent for review to the original author on the basis of the plan, BEFORE the data come in.
- Unlike standard replication attempts where the author of the published, replicated study sees it only after the results come in, we will catch the replicated author at an early stage. Many will provide constructive feedback to help perfect the planned protocol so it has the best chance of replicating the already-published target effect.
3. The results will not be presented as a “successful replication” or “failed replication”. Rarely is any one data set definitive by itself, so we will concentrate on making a cumulative estimate of the relevant effect’s size, together with a confidence interval or credibility interval.
- This will encourage people to make more quantitative theories aimed at predicting a certain effect size, rather than only worrying about whether the null hypothesis can be rejected (as we know, the null hypothesis is almost never true, so can almost always be rejected if one gets enough data).
This initiative is the latest in a long journey for me. Ten years ago, thinking that allowing the posting of comments on published papers would result in flaws and missed connections to come to light much earlier, David Eagleman and I published a letter to that effect in Nature and campaigned (unsuccessfully) for commenting to be allowed on PubMed abstracts.
Since then, we’ve seen that even where comments are allowed, few scientists make them, probably because there is little incentive to do so and doing it would risk antagonising their colleagues. In 2007 I became an academic editor and advisory board member for PLoS ONE, which poses fewer obstacles to publishing replication studies than do most journals. I’m lucky to have gone along on the ride as PLoS ONE rapidly became the largest journal in the world (I resigned my positions at PLoS ONE to make time for the gig at PoPS). But despite the general success of PLoS ONE, replication studies were still few and far between.
In 2011, Hal Pashler, Bobbie Spellman, Sean Kang and I started PsychFileDrawer, a website for researchers to post notices about replication studies. This has enjoyed some success, but it seems without the carrot of a published journal article, few researchers will upload results, or perhaps even conduct replication studies.
Finally with this Perspectives on Psychological Science initiative, a number of things have come together to overcome the main obstacles to publication studies: fear of antagonising other researchers and the uphill battle required to get the study published. Some other worthy efforts to encourage replication studies are happening at Cortex and BMC Psychology.
If you’re interested in proposing to conduct a replication study for eventual publication, check out the instructions and then drop us a line at replicationseditor @ psychologicalscience.org!
Scientists of all sorts increasingly recognize the existence of systemic problems in science, and that as a consequence of these problems we cannot trust the results we read in journal articles. One of the biggest problems is the file-drawer problem. Indeed, it is mostly as a consequence of the file-drawer problem that in many areas most published findings are false.
Consider cancer preclinical bench research, just as an example. The head of Amgen cancer research tried to replicate 53 landmark papers. He could not replicate 47 of the 53 findings.
In experimental psychology, a rash of articles has pointed out the causes of false findings, and a replication project that will dwarf Amgen’s is well underway. The drumbeat of bad news will only get louder.
What will be the consequences for you as an individual scientist? Field-wide reforms will certainly come, partly because of changes in journal and grant funder policies. Some of these reforms will be effective, but they will not arrive fast enough to halt the continued decline of the reputation of many areas.
In the interim, more and more results will be viewed with suspicion. This will affect individual scientists directly, including those without sin. There will be:
- increased suspicion by reviewers and editors of results in submitted manuscripts (“Given the history of results in this area, shouldn’t we require an additional experiment?“)
- lower evaluation of job applicants for faculty and postdoctoral positions (“I’ve just seen too many unreliable findings in that area“)
- lower scores for grant applications (“I don’t think they should be building on that paper without more pilot data replicating it“)
These effects will be unevenly distributed. They will often manifest as exaggerations of existing biases. If a senior scientist already had a dim view of social psychology, for example, then the continuing replicability crisis will likely magnify his bias, whereas his view of other fields that the scientist “trusts” will not be as affected by the whiff of scandal, at least for awhile- people have a way of making excuses for themselves and their friends.
But there are some things you can do to protect yourself. These practices will eventually become widespread. But get a head start, and look good by comparison.
- Preregister your study hypotheses, methods, and analysis plan. If you go on record with your plan before you do the study, this will allay the suspicion that your result is not robust, that you fished around with techniques and statistics until you got a statistically significant result. Journals will increasingly endorse a policy of favoring submitted manuscripts that have preregistered their plan in this way. Although websites set up to take these plans may not yet be available in your field, they are coming, and in the meantime you can post something on your own website, on FigShare perhaps, or in your university publicly accessible e-repository.
- Post your raw data (where ethically possible), experiment code, and analysis code to the web. This says you’ve got nothing to hide. No dodgy analyses, and you welcome the contributions of others to improve your statistical practices.
- Post all pilot data, interim results, and everything you do to the web, as the data come in. This is the ultimate in open science. You can link to your “electronic laboratory notebooks” in your grants and papers. Your reviewers will have no excuse to harbor dark thoughts about how your results came about, when they can go through the whole record.
The proponents of open science are sometimes accused of being naifs who don’t understand that secretive practices are necessary to avoid being scooped, or that sweeping inconvenient results under the rug is what you got to get your results into those high impact-factor journals. But the lay of the land has begun to change.
Make way for the cynics! We are about to see people practice open science not out of idealism, but rather out of self interest, as a defensive measure. All to the better of science.
Below are research presentations I’m involved in for Vision Sciences Society in May. If you’re attending VSS, don’t forget about the Publishing, Open Access, and Open Science satellite which will be Friday at 11am. Let us know your opinion on the issues and what should be discussed here
Splitting attention slows attention: poor temporal resolution in multiple object tracking
Alex O. Holcombe, Wei-Ying Chen
Session Name: Attention: Tracking (Talk session)
Session Date and Time: Sunday, May 13, 2012, 10:45 am – 12:30 pm
Location: Royal Ballroom 4-5
When attention is split into foci at disparate locations, the minimum size of the selection focus at each location is larger than if only one location is targeted (Franconeri, Alvarez, & Enns, 2007)- splitting attention reduces its spatial resolution. Here we tested temporal resolution and speed limits. STIMULUS. Three concentric circular arrays (separated by large distances to avoid spatial interactions between them) of identical discs were centered on fixation. Up to three discs (one from each ring) were designated as targets. The discs orbited fixation at a constant speed, occasionally reversing direction. After the discs stopped, participants were prompted to report the location of one of the targets. DESIGN. Across trials, the speed of the discs and the number in each array was varied, which jointly determined the temporal frequency. For instance, with 9 objects in the array, a speed of 1.1 rps would be 9.9 Hz. RESULTS. With only one target, tracking was not possible above about 9 Hz, far below the limits for perceiving the direction of the motion, and consistent with Verstraten, Cavanagh, & LaBianca (2000). The data additionally suggest a speed limit, with tracking impossible above 1.8 rps, even when temporal frequency was relatively low. Tracking two targets could only be done at lower speeds (1.4 rps) and lower temporal frequencies (6 Hz). This decrease is approximately that predicted if at high speeds and high temporal frequencies, only a single target could be tracked. Tracking three yielded still lower limits. Little impairment was seen at very slow speeds, suggesting these results were not caused by a reduction in spatial resolution. CONCLUSION. Splitting attention reduces the speed limits and the temporal frequency limits on tracking. We suggest a parallel processing resource is split among targets, with less resource on a target yielding poorer spatial and temporal precision and slower maximum speed.
A hemisphere-specific attentional resource supports tracking only one fast-moving object.
Wei-Ying Chen & Alex O. Holcombe
Session Name: Attention: Tracking (Talk session)
Session Date and Time: Sunday, May 13, 2012, 10:45 am – 12:30 pm
Location: Royal Ballroom 4-5
Playing a team sport or taking children to the beach involves tracking multiple moving targets. Resource theory asserts that a limited resource is divided among targets, and performance reflects the amount available per target. Holcombe and Chen (2011) validated this with evidence that tracking a fast-moving target depletes the resource. Using slow speeds Alvarez and Cavanagh (2005) found the resource consumed by additional targets is hemisphere-specific. They didn’t test the effect of speed, and here we tested whether speed also depletes a hemisphere-specific resource. To put any speed limit cost in perspective, we modeled a “total depletion” scenario- the speed limit cost if at high speeds one could not track the additional target at all and had to guess one target. Experiment 1 found that the speed limit for tracking two targets in one hemifield was similar to that predicted by total depletion, suggesting that the resource was totally depleted. If the second target was instead placed in the opposite hemifield, little decrement in speed limit occurred. Experiment 2 extended this comparison to tracking two vs. four targets. Compared to the speed limit for tracking two targets in a single hemifield, adding two more targets in the opposite hemifield left the speed limit largely unchanged. However starting with one target in both the left and right hemifields, adding another to each hemifield had a severe cost similar to that of the total depletion model. Both experiments support the theory that an object moving very fast exhausts a hemisphere-specific attentional tracking resource.
Attending to one green item while ignoring another: Costly, but with curious effects of stimulus arrangement
Shih-Yu Lo & Alex O. Holcombe
Session Name: Attention: Features I (Poster session)
Session Date and Time: Monday, May 14, 2012, 8:15 am – 12:15 pm
Location: Vista Ballroom
Splitting attention between targets of different colors is not costly by itself. As we found previously, however, monitoring a target of a particular color makes one more vulnerable to interference by distracters that share the target color. Participants monitored the changing spatial frequencies of two targets of either the same (e.g., red and red) or different colors (e.g., red and green). The changing stimuli disappeared without warning and participants reported the final spatial frequency of one of the targets. In the different-colors condition, a large cost occurs if a green distracter is superposed on the red target in the first location and a red distracter is superposed on the green target in the second location. This likely reflects a difficulty with attending to a color in one location while ignoring it in another. Here we focus on a subsidiary finding regarding perceptual lags. Participants reported spatial frequency values from the past rather than the correct final value, and such lags were greater in the different-colors condition. This “perceptual lag” cost was found when the two stimuli were horizontally arrayed but not, curiously, when they were vertically arrayed. Arrangement was confounded however with processing by separate brain hemispheres (opposite hemifields). In our new study, we unconfounded arrangement and presentation in separate hemifields with a diagonal condition- targets were not horizontally arrayed but were still presented to different hemifields. No significant different-colors lag cost was found in this diagonal arrangement (5 ms) or in the vertical arrangement (86 ms), but the cost (167 ms) was significant in the horizontal arrangement, as in previous experiments. Horizontal arrangement apparently has a special effect apart from the targets being processed by different hemispheres. To speculate, this may reflect sensitivity to bilateral symmetry and its violation when the target colors are different.
Dysmetric saccades to targets moving in predictable but nonlinear trajectories
Reza Azadi, Alex Holcombe, and Jay Edelman
A saccadic eye movement to a moving object requires taking both the object’s position and velocity into account. While recent studies have demonstrated that saccades can do this quite well for linear trajectories, its ability to do so for stimuli moving in more complex, yet predictable, trajectories is unknown. With objects moving in circular trajectories, we document failures of saccades not only to compensate for target motion, but even to saccade successfully to any location on the object trajectory. While maintaining central fixation, subjects viewed a target moving in a circular trajectory at an eccentricity of 6, 9, or 12 deg for 1-2 sec. The stimulus orbited fixation at a rate of 0.375, 0.75, or 1.5 revolutions/sec. The disappearance of the central fixation point cued the saccade. Quite unexpectedly, the circularly moving stimuli substantially compromised saccade generation. Compared with saccades to non-moving targets, saccades to circularly moving targets at all eccentricities had substantially lower amplitude gains, greater curvature, and longer reaction times. Gains decreased by 20% at 0.375 cycles/sec and more than 50% at 1.5 cycles/sec. Reaction times increased by over 100ms for 1.5 cycles/sec. In contrast, the relationship between peak velocity and amplitude was unchanged. Given the delayed nature of the saccade task, the system ought to have sufficient time to program a reasonable voluntary saccade to some particular location on the trajectory. But, the abnormal gain, curvature, and increased reaction time indicate that something else is going on. The successive visual transients along the target trajectory perhaps engage elements of the reflexive system continually, possibly engaging vector averaging processes and preventing anticipation. These results indicate that motor output can be inextricably bound to sensory input even during a highly voluntary motor act, and thus suggest that current understanding of reflexive vs. voluntary saccades is incomplete.
One of our first posts is addressed to the Association for Research in Personality newsletter:
Regarding your article entitled “Personality Psychology Has a Serious Problem (And so Do Many Other Areas of Psychology)”,
We agree wholeheartedly with your diagnosis of a major problem in publication practices in psychology. As you explain, any solution has to include a reduction in the systematic bias against publishing non-replications that now exists. Such a bias seems to be present in the editorial practices of all of the major psychology journals. In addition, discussions with colleagues lead us to believe that investigators themselves tend to lose interest in a phenomenon when they fail to replicate a result, partly because they know that publishing negative findings is likely to be difficult and writing the manuscript time-consuming. Given these biases, it seems inevitable that our literature and even our textbooks are filling with fascinating “findings” that lack validity. Read the rest at the PsychFileDrawer blog.
Any ideas for enticing people contribute replication attempts to PsychFileDrawer will be gratefully received!
Bradley Voytek spotted a disturbing question in an official “Responsible Conduct of Research” training program:
This defense of the status quo has no place in a “Responsible Conduct of Research” training program. It reads like the old guard self-interestedly maintaining the current system by foisting unjustified beliefs onto young researchers!
The part that bothers me the most is the sentence “It is likely that the peer review process will evolve to minimize bias and conflicts of interest”. What is the evidence for this?
Has the process been evolving to minimize bias and conflicts, or to increase them? I don’t think the answer is very clear. As counterweight to the official optimistic opinion, here are a few corrupting influences:
- Pharmaceutical companies continue to buy influence with medical journals, by buying hundreds of copies of journal issues that run studies that support their products.
- Pharmaceutical companies continue to ghostwrite journal articles for doctors, to plant their views in the medical literature.
- Scientists of every stripe often fail to disclose their conflicts of interest.
- Journals develop new revenue streams, like fast-tracking articles for a fee, that may open them to favoring the select authors who pay.
- Many reviewers are, like most humans, biased towards their own self-interest. This can yield a bias to recommend rejection of papers by rivals. Because reviewers in most journals are anonymous, they are never held to account.
- Journals don’t have the resources to investigate authors accused of fraud, and universities often try to avoid finding fault with the researchers they employ.
Many people have suggested partial remedies to these problems, but it’s an uphill battle to implement them, due to the slow pace of change in the journal system. We have to remember this and not be lulled into complacency by the propaganda seen in that training program. It was created by an organization of academics called CITI.
UPDATE: In the comments below, Jason Snyder pointed out an article from CITI in which CITI reports that over 6,000 researchers a month are taking this course — being subjected to this biased question. Some of us object not only to their characterization of the peer review process, but also to their suggestion that blogs are not a good place to do science. We don’t want thousands of researchers to continue to be forced to assent to the conservative opinion articulated by CITI, so we’re drafting a letter asking them to delete the question.
The transmission of new scientific ideas and knowledge is needlessly slow:
|Journal subscription fees||Open access mandates|
|Competition to be first-to-publish motivates secrecy||Open Science mandates|
|Jargon||Increase science communication; science blogging|
|Pressure to publish high quantity means no time for learning from other areas||Reform of incentives in academia|
|Inefficient format of journal articles (e.g. prose)||Evidence charts, ?|
|Long lag time until things are published||Peer review post publication, not pre publication|
|Difficulty publishing fragmentary criticisms||Open peer review; incentivize post-publication commenting|
|Information contained in peer reviewers’ reviews is never published||Open peer review or publication of (possibly anonymous) reviews; incentivize online post-publication commenting|
|Difficulty publishing non-replications||Open Science|
UPDATE: Daniel Mietchen, in the true spirit of open science, has put up an editable version of this very incomplete table.
This is something science aspires to in evaluating manuscripts for publication. In fact it’s fundamental to the integrity of science- when you read an article in a scientific journal, the idea is that you should know that the article went through the same review process as all the others.
The science you see in a prestigious journal is not there because the authors paid more than others did, but rather because the science was evaluated as high quality on its own merits. There are flaws in the process, such as the bias that occurs because usually the reviewers know who the manuscript authors are, but at least there’s no real money involved- nothing as meretricious as some cash to grease the wheels.
But now money has started to infiltrate the system. Several journals are now accepting money for “fast-track” services. It is hard to see how this policy can be implemented without sometimes giving the monied authors an advantage over those who don’t pay. Fast-tracking seems likely to leads to shortcut by the editor or reviewers as they seek to meet the fast-tracking deadline. And it seems these journals won’t even indicate which manuscripts benefited from fast-tracking and which didn’t.
Please join us in signing an open protest letter that we’ll soon send to these journals.
I recently learned that a journal called Obesity Reviews has a “Fast Track Facility”:
A submission fee of $1,000 or £750 for articles up to 9000 words long, or $1500 for articles more than 9,000 words long guarantees peer-review within 10 working days
This is a terrible development for academia. It creates a two-tier system, wherein scientists who are well-funded such as those from rich countries now have an unfair advantage over those who don’t. Science traditionally has been a partial refuge from the injustice of rich vs. poor. Although of course it was never entirely insulated from it, scientific institutions and journals have in the past have tried to treat all authors similarly.
To some, this “Fast Track Facility” may seem similar to the system of open-access journals where authors pay a fee to have their article published if it passes peer review. At least in the case of PLoS ONE (the open-access journal I am an editor for), however, this is very different because PLoS ONE waives the fee for authors who cannot pay. Authors who cannot pay are treated the same as authors who can pay. The “Fast Track Facility” policy of Obesity Reviews violates this fundamental principle of fairness.
UPDATE: Help write and sign on to a protest letter
Previously, the Australian Research Council (ARC) expressly forbade use of grant funds to pay publication charges. This prevented many of us from publishing in open-access journals, as they generally charge a fee.
Fortunately, the newly-revised funding rules change that, and instead strongly encourage open access, via journals and via depositing one’s research in an institutional repository.
5.2.2 Publication and dissemination of Project outputs and outreach activity costs
may be supported at up to two (2) per cent of total ARC funding awarded to
the Project. The ARC strongly encourages publication in publicly accessible
outlets and the depositing of data and any publications arising from a
Project in an appropriate subject and/or institutional repository.
13.3.2 The Final Report must justify why any publications from a Project have
not been deposited in appropriate repositories within 12 months of
publication. The Final Report must outline how data arising from the
Project has been made publicly accessible where appropriate.
If you have ideas of how this should be made stronger for future years, let me know and maybe we can sign a letter to the ARC together. It would be good to move towards a mandate, as suggested by the people of open access week.
Quodlibet is an obscure word that originally referred to a medieval event that included a debate. I haven’t been able to find much information about it, but here is a brief description from Graham (2007):
Beginning in the thirteenth century, quodlibets were a part of the academic program of the theology and philosophy faculties of universities… The first of the two days of the quodlibet was a day of debate presided over by a master who proposed a question of his own for discussion.
I’m interested in this because I rue the lack of debates in modern science. Perhaps it’s only an accident of history that real debates aren’t happening much nowadays.
Also during the quodlibet, according to Graham, the presiding master “accepted questions from anyone present on any subject and answers were suggested by the master and others.” Sounds like a blend of the unconference (1,2) and what we think of as a traditional debate.
We’ve created evidencechart.com as a way debating might be revived in a compact online form. However, we’re still working on the adversarial form of evidence charts designed especially for debating. Let me know if you’re interested in participating.
Graham, BFH (2007). Review of Magistri Johannis Hus: Quodlibet, Disputationis de Quolibet Pragae in Facultate Artium Mense Ianuario anni 1411 habitae Enchiridion. The Catholic Historical Review, Volume 93, Number 3, pp. 639-640.