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Alex Holcombe
Works at University of Sydney
Attended Harvard University
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Alex Holcombe

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congrats to the journal Cognition for instituting a data posting requirement!  Only thing is it's copyrighted like most things in the journal so you can't read it- perhaps on oversight. But I'll (illegally) paste it here:

 I will also be instituting a data transparency policy. To
encourage meta-analysis and to help everyone understand
data better, authors of all published papers will be asked to
make their raw data publically available (unless doing so is
prohibited for some good reason). Here is the specific policy
that I plan to institute:
i. All empirical papers must archive their data upon
acceptance in order to be published unless the
authors provide a compelling reason why they cannot
(e.g., expense, confidentiality). The action editor
will be the final arbiter of whether the reason is suf-
ficiently compelling.
ii. ‘‘Data’’ refers to an electronic file containing nonidentified
responses that are potentially already
coded. Normally, the data would represent an early
stage of electronic processing, before individual
responses have been aggregated. The data must be
in a form that allows all reported statistical analyses
to be reproduced while retaining the confidentiality
of individual participants. This entails that the data
are formatted and documented in a way that makes
the structure of the data set readily apparent.
iii. Archiving consists either of submitting the data to
the journal (to be displayed as supplementary material
at the end of the article), sending it to some
other archive that is accessible to established
researchers and maintained by a substantial established
institution, or authors making the data available
on their own website, assuming that they can
assure us the site will be maintained by a recognized
institution for a reasonable period of time. Again,
action editors will be the final arbiters of the appropriateness
of an archive.
iv. Any publication that reports analyses of or refers to
archived data will be expected to cite the original
publication in which the data were reported.
v. This policy is new and therefore open to modification.
Our aim is to implement a policy that maximizes
transparency while minimizing the burden
on authors.
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Alexander, name from the Gods's profile photo
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Its alrwady been published hasn't it, in some ways you have stuck up for me and I thank you for that.
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Alex Holcombe

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Lock wasn't talking about the use of impact factor and journal brand, but he could have been:

Grahame Lock, a fellow in the faculty of philosophy at Oxford University, says that a managerial "hyper-bureaucracy" has taken hold in higher education. "Imagine that managers are going to assess the quality of restaurant meals but they have no sense of taste," he says. "They have no idea – everything tastes the same to them. So what are they going to do?

"They will undertake evaluations such as how many minutes did it take for the soup to arrive at your table? How many words of explanation did the waiter use? And so on."

http://www.theguardian.com/education/2010/mar/30/academic-bureaucracy-rise-managers-higher-education
Figures show a 33% increase in the number of managers in higher education in the last five years. Why has this happened?
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Alex Holcombe

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Professor Stephen Curry of Imperial College, London is giving a Sydney Ideas lecture next Monday (http://whatson.sydney.edu.au/events/published/sydney-ideas-professor-stephen-curry) on X-ray crystallography.

He has also agreed to present on "Why open access matters". He plans to give a short talk to allow plenty of time for discussion.

Where: New Law Annexe Seminar Room 446, Camperdown, University of Sydney
When: 4:30 to 5:30 pm, Monday 18 August 
This is a public lecture- no tickets, no bookings.

Professor Curry has written about open access for The Guardian (http://www.theguardian.com/profile/stephen-curry) and his personal blog (http://occamstypewriter.org/scurry/). His comments are sometimes robust- such as on the topic of journal impact factor (http://occamstypewriter.org/scurry/2012/08/13/sick-of-impact-factors/), so I expect this will be a stimulating talk.

Contact: alex.holcombe@sydney.edu.au
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Alex Holcombe

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Robert P. O'Shea's profile photo
 
This could be a good documentary to which to refer beginning students.

Advantages:
It features John Mollon, Edwin Land, and Semir Zeki.
It is simple.
It explains the theories of colour vision circa 1985.

Disadvantages:
It has some chunks missing.
It is from circa 1985, referring to technology that today's students might not be familiar with (film, CRT TVs).
The explanation of coloured afterimages is too compressed.
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Alex Holcombe

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"Vision Research (ELS) Request to Review:
Hi Alex,
I know this is a long shot, given your dedication to open access journals. Your article (linked from your web page) is really on point, and the times they are a changing. If I didn't have such a life long fondness and respect for Vision Research I would quit the editorial board. However, if you would be willing to give free labor once more to this hugely profitable cartel, I would appreciate it. Or suggestions if you have any.
cheers,
[a Vision Research editor]"
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Alex Holcombe's profile photoJP de Ruiter's profile photoMike Taylor's profile photo
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Yes, it certainly is ridiculous. See my very first mainstream-media article on open-access issues, Peers, review your actions at http://www.timeshighereducation.co.uk/417576.article
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Edge 2014 question: What scientific idea is ready for retirement? Me: idea that Science is Self-Correcting. http://t.co/gfJva3pg75 You can't comment on the #EdgeQ   site, but I'd love to hear comments (e.g., here) 
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Matt McIrvin's profile photoOpen Science's profile photo
 
Good essay, though I suppose actually retiring the idea of self-correcting science would mean giving up on science entirely, not doing things to fix the situation.
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Alex Holcombe

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Today's reply to an #Elsevier  review request:

Dear Professor XXXX,

Traditional scientific publishers make higher profits than almost every other legal industry, by exploiting scholars' free labor and draining university library funds. Rather than reviewing for Elsevier, I have pledged to spend my time supporting alternatives, such as open access journals. 

The UK Open Access Implementation Group (http://t.co/rhgKN1bGqa) exists to help scholarly societies transition to alternative publishing models. Vision Research has a venerable history of publishing high-quality perception research, and almost all the credit in my opinion goes to the editorial board and the reviewers, who have added a lot of value over the years by improving the quality of authors' research through the reviewing process. My recommendation is for the editorial boards of Elsevier-published journals to resign and pursue alternatives. 

best
Alex

https://alexholcombe.wordpress.com/2013/01/09/scholarly-publishers-and-their-high-profits/
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The "show me how to cite" Wikimedia image functionality is fabulous to have, but could be improved a bit. Like for this image, CC-BY-SA, it says "you need to attribute the author" and when you click on "show me how", it says you should do it like this:

"Ventral-dorsal streams". Licensed under Creative Commons Attribution-Share Alike 3.0 via Wikimedia Commons - http://commons.wikimedia.org/wiki/File:Ventral-dorsal_streams.svg#mediaviewer/File:Ventral-dorsal_streams.svg

But there's no author indicated! Does that mean a good Wikipedia-person made the image and isn't asking for attribution? Seems like the "show me how" thing ought to know when there's an author to credit and when there isn't +Daniel Mietchen 

http://en.wikipedia.org/wiki/Two-streams_hypothesis#mediaviewer/File:Ventral-dorsal_streams.svg
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Rich FitzJohn's profile photoRobert P. O'Shea's profile photo
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Dear +Alex Holcombe, You can find the author of a Wikipedia image by:
     Clicking on the image.
     Clicking on the arrow at the bottom of the screen for more details. This will take you to the Wikimedia Commons page where the image is stored.
     Clicking on the link on the resultant page called "More details about this file".
     Scrolling down to File History.

In this case, you see that the original author was "Selket", with a some tweaks from "Profil".
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Alex Holcombe

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Are you in violation of the Declaration of Helsinki? [Scholarly publishing pro-tip]

In 2013, the following phrase was added to the Declaration: “Every research study involving human subjects must be registered in a publicly accessible database before recruitment of the first subject”. 

Many journals, such as the Journal of Vision and I think PLoS ONE, require that when submitting a manuscript you check a box indicating compliance with the Declaration of Helsinki. So if you publish in such journals and don't pre-register your study in a publicly accessible database, I'll see you in Hell / the Hague!  

For older research, you can try something like this: "The protocol was approved by the ethics committee of the University of Sydney in accordance with the Declaration of Helsinki (pre-2013 version; the late 2013 version’s statement that “Every research study involving human subjects must be registered in a publicly accessible database before recruitment of the first subject” appeared after this research was completed)."

The weird thing is that Helsinki didn't specify what they meant by registration, but they were probably thinking of the problem of clinical trials and publication bias. E.g., trials that are disappeared when they yield an outcome that a sponsoring pharma company is not happy with. So maybe they were trying to get people to at least describe the study enough that it could be found later by meta-analysis authors. See alltrials.net

Although I think study registration should be optional rather than required, for my area the main advantage I see of it (or more specifically, registration of the data analysis plan) is  protection against suspicion of p-hacking. Here are some details: 
http://neurocritic.blogspot.com.au/2013/07/demerit-badges-for-non-preregistered.html
http://www.psychologicalscience.org/index.php/publications/journals/psychological_science/badges 
http://centerforopenscience.org/journals/  
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Alex Holcombe's profile photoMatt Hodgkinson's profile photo
 
+Matt Hodgkinson has provided some additional info on twitter:
Not the best update to the Declaration of Helsinki... 1. They plainly mean trials, not all human subject research.
2. Alltrials & PLOS journals allow trial registration after 1st participant since last year http://blogs.plos.org/speakingofmedicine/2013/08/13/full-registration-and-reporting-of-all-trials-at-plos-medicine/

New DoH says "Researchers have a duty to make publicly available the results of their research on human subjects"
DoH: "Negative and inconclusive as well as positive results must be published or otherwise made publicly available"
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Alex Holcombe

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Our university is trialling an Electronic Lab Notebook software, LabArchives. Someone asked me why I won't be using it, FYI here's my answer.

I'm more inclined to support open-source solutions. But open-source type solutions are currently harder to use I think, so for those who don't have the technical know-how and don't have time to acquire such skills, LabArchives may be the way to go.

For myself, I favor Github and also Open Science Framework for code and data archiving, and also for code management in the case of github.  For example, for the project I'm currently working on, I'm in a data analysis phase and am using github for all the version control through R, here: https://github.com/alexholcombe/speed-tf-VSS14 .

For archiving data, I'm currently inclined to use Open Science Framework, e.g. program code and data for experiments associated with an in-revision paper is here : https://osf.io/t4vmy/
OSF actually doesn't require technical know-how at all (although they're adding integration with github, which I may use in future), but it's mainly just a place to drop files currently.

Neither GitHub nor OSF have daily-lab-notebook type functionality, but I don't need that because all the parameters and details associated with running a subject in an experiment are automatically saved by my PsychoPy program when I execute it, including a frozen copy of the code at the time it was run and system info.  For those using equipment not integrated together, like say a neuropsychological test done with paper and pencil, an EEG run somewhere else, and a behavioral test, a lab notebook might make more sense.
speed-tf-VSS14 - Speed limits, and relation to temporal freq limits on attentional tracking. VSS2014
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Brian Glanz's profile photoHaroon Rasheed's profile photoGuy Bilodeau's profile photoDarren Finlay's profile photo
 
As you know we use LabTrove, an open source alternative, but I think sometimes large organisations prefer software as a solution as opposed to something with the promise/threat of long-term investment in, for example, actually developing software. It's interesting that the lab notebook in Chemistry is traditionally like a diary - the entries are in date order and I think subconsciously we sort the experiments along a timeline ("I remember I did that experiment back in December"), but with a move to electronic the book is finally searchable - joy. I guess I'm surprised you don't do the same for e.g. testing flashy colours on people, i.e. "Today subject X was unable to distinguish colours at Y rpm, unlike last week when Z happened."
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Hi +Open Source Malaria , do you have an explicit license for your data beyond saying CC-BY?  

The Open Knowledge Foundation has created the Open Data Commons Attribution License (ODC-BY, http://opendatacommons.org/licenses/by/summary/), and it is roughly what we want for data associated with the Registered Replication Reports (RRR) article type of Perspectives on Psychological Science.  

I am not clear on whether there is any difference between conventional CC-BY and ODC-BY, perhaps there's not.

For RRRs, the data collected by each lab is posted on their respective OSF pages.  Our policy is still in discussion but may end up being that other researchers can use the data freely, but only after the RRR has been published-  an embargo on use of the data. This is not an option with ODC-BY, although perhaps an informal add-on clause would be sufficient.  
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Don't know. Appears similar - is there a need for two things?
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"Sperling, 1963. Human Factors, 5, 19-31 --one of the five most cited articles in the history of the journal). An interesting sidelight is that this research was carried out in the Psychology Department after I had been failed by Harvard's Social Relations Department and was not permitted to carry out the project I had originally planned." http://www.opt.uh.edu/files/opticalSociety/2013_OSA_VM_Program.pdf
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Work
Employment
  • University of Sydney
    Associate Professor, present
Basic Information
Gender
Male
Story
Tagline
Academic. Doing basic research, and improving the system of science.
Introduction
Education
  • Harvard University
    Psychology, 1995 - 2000
  • University of Virginia
    Cognitive Science, Psychology, 1991 - 1995