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Alex Holcombe
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Alex Holcombe

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In Nature Publishing Group's Scientific Reports reviewer form, after a series of questions about the quality of a manuscript and its presentation, there is one and only one question that at all alludes to questionable research practices/fraud/deception/:  

 "Electrophoretic gels and blots are presented clearly and are free from apparent manipulation?"

 I guess they think gel and blot manipulation is a huge problem, to single it out from all the other questionable practices that go on. (The manuscript I reviewed was in psychology, so the question had no relevance).  Would be nice to see a mention of p-hacking, since something like that is widespread across many areas of science.
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"viewed scotopically, objects look light and dark, but not gray. Turning the lights down is not like changing a color image to a black-and-white one." I think they mean that you do experience gradations of light and dark... but not gray, which is implicitly chromatic, or the absence of chromaticity in a colorful world.  I never thought about that! From my memory of scotopic experience, it may be true. http://web.mit.edu/abyrne/www/colorblind.pdf
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Why are action potentials in animals and plants all-or-none? 

I haven't found anything that explains this, so I've written the below for use in lecturing undergrads. I'd welcome any comments, corrections, or links to other explanations.

The all-or-none nature of the action potential is how we can achieve long-range transmission without degradation of the signal.
-The signal is binary or digital; no action potential or yes an action potential; like 0 or 1, nothing in between.
-Imagine that it was instead analog, a graded signal instead of digital.
-The neuron might have a signal of, say,60 millivolts, travelling down the axon. You need to preserve the 60-mv msg all the way to the destination.
-So each bit of the neuron has to generate the mV that the previous bit generated. 
-But the problem is you get errors, and the errors accumulate, just like in the Chinese whispers game.
-The second millimetre might be affected by random fluctuations and generate 61 mV. The third mm should then generate 61 mV but erroneous fluctuations might have it go to 63 mV. So, who knows what the message will be by the time it reaches the end of the axon.
-This man Claude Shannon had the insight that if you use digital, you can have perfect transmission, no errors.
-Instead of each bit of the neuron set up to try to reproduce the level in the previous bit of neuron,
it’s set up only to detect whether the membrane potential reaches higher than a threshold, and if the electrical potential is greater than that, it creates a predetermined signal.
-The threshold can have a value related to the size of random fluctuations, greater than the random fluctuations, in which case an action potential is never generated in error, and never erroneously not generated.
-Shannon proved all this in his master’s thesis, the greatest master’s thesis in history. It led to all the digital electronics that we use today.

*If you're wondering about the mention of plants, many plants do indeed have action potentials: http://onlinelibrary.wiley.com/store/10.1111/j.1365-3040.2006.01614.x/asset/j.1365-3040.2006.01614.x.pdf;jsessionid=37878CEAC4D234280FB73E9BF27694CE.f01t04?v=1&t=i8o4o3x7&s=ebf6e66ce48f988202c04bb15a028a07b9c52bcf
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Excellent info, thanks +Jonathan Hunt 
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4th-century St. Ambrose read silently- St. Augustine wrote: “When he read, his eyes scanned the page and his heart sought out the meaning, but his voice was silent and his tongue was still.” Some scholars have taken this passage as evidence that people at that time typically read aloud. That hypothesis matches the fact that punctuation was then used only sporadically; vocalizing would help the reader hear the prosody.

Willingham, Daniel T. Raising Kids Who Read: What Parents and Teachers Can Do (Kindle Locations 2657-2659). 

also see: http://web.stanford.edu/class/history34q/readings/Manguel/Silent_Readers.html
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Reviewing instructions for the journal Psychological Science which probably started last year. More Methods reporting, part of effort to improve reproducibility.

(1) Manuscript Evaluation Criteria. Editors and reviewers alike are now asked to evaluate submissions with three questions in mind: (a) What will the reader of this paper learn about psychology that she or he did not know (or could not have known) before? (b) Why is that knowledge important for the field? (c) How are the claims made in the article justified by the methods used? Manuscripts that provide clear and compelling answers to these “What,” “Why,” and “How” questions will have the best prospects of being accepted for publication. For background on the rationale for these questions, please see this editorial: http://pss.sagepub.com/content/early/2013/11/25/0956797613512465.full/

2) Enhanced Reporting of Methods. Another new feature of the manuscript submission process for 2014 is a section containing checkboxes for four Research Disclosure Statement items (very similar to existing items confirming that research meets ethical guidelines, etc.). Submitting authors must check each item and, in doing so, actively declare that:

(a) the total number of excluded observations, and the reasons for making these exclusions, have been reported in the Method section(s),

(b) all independent variables or manipulations, whether successful or failed, have been reported in the Method section(s) [Authors skip this step if there were no independent variables or manipulations, as in the case of correlational research.],

(c) all dependent variables or measures that were analyzed for this article’s target research question have been reported in the Methods section(s), and

(d) the Method section(s) describe how sample size was determined and the rule for stopping data collection

As a reviewer, you don’t need to worry about the checkboxes or anything else to do with the manuscript submission process. The key point here is that the manuscript you’ll be reading will contain four categories of methodological details—Exclusions, Manipulations (if any), Measures, and Sample Size—that have not required disclosure under past reporting standards (of Psychological Science in particular or psychology journals in general) but that are important for interpreting research findings. I hope you will find these methodological details helpful to you in evaluating PSCI-15-0379.

(3) New Word Limits. For manuscripts submitted after January 1, 2014, the Method and Results sections of a manuscript will be excluded from the word limits on Research Articles and Research Reports. The new limits on Research Articles and Research Reports will be 2,000 and 1,000 words, respectively, and will include introductory and Discussion sections, as well as notes, acknowledgements, and appendices. The purpose of eliminating strict limits on the Method and Results sections is to afford authors the opportunity to report what they did, and what they found, in a manner that is clear, concise, and complete (see more details here: http://www.psychologicalscience.org/index.php/publications/observer/2013/november-13/whats-new-at-psychological-science.html). I welcome any ideas you may have for improving the exposition of the paper you’re reviewing.

(4) Embracing the “New Statistics.” Psychological Science now recommends the use of the “new statistics”—effect sizes, confidence intervals, and meta-analysis—to avoid problems associated with null-hypothesis significance testing (NHST). The journal sought to aid researchers in shifting from reliance on NHST to estimation and other preferred techniques by publishing a tutorial by Geoff Cumming, a leader in the new-statistics movement, that includes examples and references to books, articles, software, and online calculators that will aid authors in understanding and implementing estimation techniques in a wide range of research settings. The tutorial is available here: http://pss.sagepub.com/content/early/2013/11/07/0956797613504966.full.
Please note that the journal recommends, but does not require, adoption of the new-statistics approach. In certain areas of research—for instance, function magnetic resonance imaging (fMRI) when a brain region of interest hasn’t been pre-identified—NHST methods of analysis may be more appropriate.

(5) Supplemental Online Material. Since January 2012, Psychological Science has allowed the online publication of two types of supplemental material. One type, referred to as SOM-R, includes material that has undergone both an initial review (by two members of the editorial team) and an extended review (by two or more external referees). The other type, SOM-U, includes unreviewed material, or information that has not been vetted by either the editors or the external referees.
The distinction between the two types of supplemental material is discussed in greater detail here (http://www.psychologicalscience.org/index.php/publications/journals/psychological_science/ps-submissions#SM). Here let me emphasize two key points. First, feel free to skip over any SOM-U material that the author may have uploaded, but please look carefully at any SOM-R material. Second, in the Submission Guidelines, authors are advised that the editors take the adjective “supplemental” seriously: both SOM-R and SOM-U should include the sort of material that enhances the reader’s understanding of an article but is not essential for understanding the article. Thus, should you come across any SOM-R material you consider essential, please mention that in your review, so that the authors will know to move the material into the main article.
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Timing & Time Perception Reviews, an #openaccess journal with no fees for authors. See, free  #openaccess  can be done! -they use Open Journal Systems free software as the publishing platform, with support by Brill and from Groningen University. http://rjh.ub.rug.nl/index.php/ttpr/issue/view/1674 …
Review journal on all topics associated with timing and temporal cognition.
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Alex Holcombe

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 I plot and fit my psychophysical data using R with code I wrote over the last several years. But +Dani Linares has produced an R package, quickpsy  (https://github.com/danilinares/quickpsy), that is much cleaner and more modern than my hodgepodge of code. I'm switching to using it now. An added plus is that in using and refining it, I'm contributing to an open source codebase that other psychophysicists can easily use.
quickpsy - quickly fits and plots psychometric functions for multiple conditions
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Thanks for sharing! That looks really useful.
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A stumbling block for  #openscience  is the need to anonymise participant identities before posting their data. While many people have written about how they integrate open science into lab practices, I haven't seen much on anonymising data.

My R program anonymises my participants' data using an encryption key that I read in from a second file. This allows me to keep a project's experiment code, analysis code, and raw data all in a single git repository that github keeps track of and makes available online.  

The "loadAnonymiseSaveData.R" https://github.com/alexholcombe/MOTcircular/blob/master/dataRaw/loadAnonymiseSaveData.R file finds all the raw data files and de-identifies them when combining them. The participants are still kept separate but they are assigned new names using an encryption key read from a separate, non-public file (its name is listed in .gitignore so that git won't archive it). The use of an encryption key means the participants can be re-identified later by those who are given the key, so I can track things back all the way to the original untouched files generated by the experiment. A full audit trail like this is important for checking for errors (and fraud).

After this anonymisation step, the R files in my analysis folder https://github.com/alexholcombe/MOTcircular/tree/master/analysis analyse the anonymised data file, and all this can be viewed or downloaded by anyone, even while I am still collecting data.

Obviously, if you aren't ready to use git, this isn't going to help you. Software Carpentry (https://software-carpentry.org/) provides free classes to bring researchers up to speed.
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Hey Tom, yes and to clarify, in this example I take the subjects' initials and encrypt them into a new, fake initials which appears inset into the graph of each participant's data, psychophysics style. As I look at the data, I start to pick up on who is who, but people I show the data to, and eventual readers of the paper, can't work out who had the embarassingly low thresholds etc.

While I agree it seems innocuous to reveal authors and lab members and consenting undergraduates initials in the plots, as vision researchers have done for a century, unfortunately I can't see that any ethics or IRB panel would be eager to approve that practice!

Rather than simply eliminating the initials, encrypting them seems like a good way to do it because I can quickly work out who is who.
 
Because I only recently started doing this, I'm using a simple, rather breakable rotate-through-the-alphabet code (it's at the end of that R file), I ought to do something fancier.

I wanted to link to a best-practice document but don't know of any. However, I know there is a PLoS ONE paper in press (can't remember the author's name) on the issue of anonymising participant data and posting it, which I am keen to read.  I'd be interested to hear what you end up doing.
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Something new I'm putting under my signature when I review manuscripts for journals:

Signed (I sign all my reviews),

Alex Holcombe

To improve the transparency of peer review and editorial decisions, I avoid entering anything in boxes like the "Confidential Comments to the Associate Editor"  provided here. Also I am concerned that such boxes can easily be abused with "stealth rejections" and/or unsupported insinuations.
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Agreed -- those boxes shouldn't exist. The only thing more frustrating than rejection after bad reviews is rejection after (seemingly) positive reviews. What's the point of feedback that the authors can't see?
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Nature Scientific Reports adopts fast-tracking fees. We protested this policy at several other journals 4 years ago, our concerns appear to have caused some journals to drop it https://alexholcombe.wordpress.com/tag/fast-track-fees/
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This interacts particularly badly with things like REF. Now UK researchers can use REF income to pay fast-tracking fees to get outputs to get REF income. I mean that's what research funding is for ...
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End of my review of a manuscript for a journal. I expect to re-use this, some of you might say something similar in your own reviews:

"Especially in cases like this where there are a lot of possible interactions that might occur and Bonferroni can really kill one's statistical power, I recommend (for future studies) preregistering one's hypotheses and analyses so that the post-hoc tests don't have to be post-hoc.

Also, I don't like papers where the (anonymized) data are not made available. But I know that's not the norm (yet).

Signed,
Alex Holcombe (I sign all my reviews)"

...Can't remember the name of the website that invites people to go much further than this and refuse to review manuscripts for which the data and code aren't posted.
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Hi Michael,
thanks for the comments!
I had forgotten that Bonferroni is too severe, thanks for the reference.

About the idea that hypothesis and analysis plan preregistration stifles exploration, that's a common belief. But the way it should be implemented (and has been implemented at the several journals, https://osf.io/8mpji/wiki/home/,  that have adopted it as an option) is to not stop post-hoc unregistered analysis. One is free to report that as normal. It simply gives the reader the assurance that the p-values of those analyses that were preregistered can be taken at face value, rather than having to worry about how much to correct for multiple comparisons and the greater worry of whether everything was p-hacked. Here's a summary of registered reports with some refs if you haven't seen it http://www.theguardian.com/science/head-quarters/2014/may/20/psychology-registration-revolution .

Finally, I like the way you put "If you can't think of a plausible alternative to your hypothesis, is it worth testing?" - there are far too many sub-fields of psychology where a statistically significant rejection of the null is the primary, even the only goal. But the null hypothesis is practically never true! Too few appreciate that we should be striving to have our theories make predictions, not binary predictions, but actual sizes of effects.
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Researchers frequently claim that motion-blind patients see moving objects as a series of stills (e.g. Ned Block here: http://www.lscp.net/persons/dupoux/papers/Kouider_Dupoux_2007.Partial_awareness_&_phenomenal_consc.BBS.pdf). However I haven't been able to find a report where the patient is clearly indicating that their experience is a series of stills rather than a blur, as would be seen with a long photographic exposure. And this is an important issue for the debate about discrete vs. continuous processes in perception. The famous Zihl akinetopsia paper is silent on this for patient L.M., but they do say that a patient described only in German by Potzl & Redlich felt a moving object appears "as if the visual stimulus remained stationary but appeared at different successive positions". That sounds like a series of stills but no indication of whether the patient was asked whether the successive positions are discrete, with empty space in between or instead might form a continuum, a blur. If anybody has a library with access to Wiener Klinische Wochenschrift, the 1911 volumes, I could ask someone in German to read the original.
In the case of certain psychoactive drugs, perhaps it is clear that a series of stills is seen rather than a blur-trail http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001056 
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This palinopsia review paper clearly makes the distinction between stroboscopic and blurred multiple images, and claims that multiple patients with palinopsia with or without akinetopsia report stroboscopic images, discrete copies of the image of the moving object. I haven't had time to read the original case reports yet to verify this. http://www.surveyophthalmol.com/article/S0039-6257%2814%2900128-3/abstract Thanks +Patrick Goodbourn 
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    Associate Professor, present
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Academic. Doing basic psychology and perception research; facilitating improvements to system of science.
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  • Harvard University
    Psychology, 1995 - 2000
  • University of Virginia
    Cognitive Science, Psychology, 1991 - 1995
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