Profile

Cover photo
Alex Holcombe
Works at University of Sydney
Attended Harvard University
Lives in Sydney
1,023 followers|110,924 views
AboutPostsPhotosYouTube

Stream

Alex Holcombe

Shared publicly  - 
1
1
Jiří Lukavský's profile photo
Add a comment...

Alex Holcombe

Shared publicly  - 
 
Collecting pro-openness, reproducibility, transparency, anti-p-hacking reviewer best practices here, please add yours, and your comments: https://docs.google.com/document/d/1gG06IrUKJI2Nzul53txZ3W2HjzpzNlsJWOHFyuJ-HKc/edit?usp=sharing
Drive
Reviewers: suggested practicesREDUCING P-HACKING, MAKING P-VALUES INTERPRETABLE In accordance with the movement towards greater transparency in reporting of studies, I suggest the authors add something like "We report how we determined our sample size, all data exclusions (if any), all manipulations, and all measures in the stud
3
1
Mark C. Wilson's profile photoDavid Roberts's profile photo
 
I think this should develop into a companion for these: https://osf.io/9f6gx/
Add a comment...

Alex Holcombe

Shared publicly  - 
 
Trying out an argument I might make in tomorrow's talk (http://www.eventbrite.com.au/e/reclaiming-the-knowledge-commons-the-ethics-of-academic-publishing-and-the-futures-of-research-tickets-17560178968):
---------- 
Used to be that a journal article was a completely stand-alone entity. 
If you wanted to know about that research, you had to get access to and subscribe to the article. The article was always just a data summary, with spin. 

Increasingly, now, in the open web one finds:
1. the data behind the paper
2. post-publication commentary
3. re-analyses

There is sometimes approximately as much information in this "grey literature" around the article as there is in the article itself. As these additional information sources grow in importance, the article's relative importance diminishes.

And it becomes more obvious that scholars need to link to, re-use, and remix individual figures, individual numbers, and individual claims in the article. Subscription access is, then, increasingly awkward- it hinders each of these, plus 1, 2, and 3 above.
Symposium program: 9:00-10:45 Session 1: Corporatisation and the commercialisation of knowledge 11:15-1:00 Session 2: Democratising knowledge or selling the farm? Varieties of 'Open Access', and the possibilities of the new digital commons 2:00-4:00 Session 3: Taking up the challenge of ethical academic publication Speakers include: Emeritus Professor Stephen Leeder, Professor Paul Komesaroff, Associate Professor Andrew Bonnell, Dr John Byron...
2
Nick Brown's profile photo
 
You also increasingly find the final draft of the article itself, or even the preprint.
Add a comment...

Alex Holcombe

Shared publicly  - 
 
"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
1
Add a comment...

Alex Holcombe

Shared publicly  - 
 
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
2
Ricky Grewal's profile photoJonathan Hunt's profile photoSam Schwarzkopf's profile photoAlex Holcombe's profile photo
5 comments
 
Excellent info, thanks +Jonathan Hunt 
Add a comment...
Have him in circles
1,023 people
Hai Kou Zhen's profile photo
Antonio Kabeluchi's profile photo
Eva Sands's profile photo
David T. Walker's profile photo
MBBS ADMISSION Radiant Education Consultants's profile photo
Matt Patten's profile photo
Anthony Barnhart's profile photo
Richard Kidd's profile photo
Steve Hughes's profile photo

Alex Holcombe

Shared publicly  - 
 
Humans and other animals are very temporally myopic. It is very difficult to learn contingencies where the delay involved is more than a few seconds or minutes (e.g. Logue, 1979).

The main reasons may be (I am doing some theoretical work on time) that: 
1)  the overwhelming majority of ecologically-relevant causality reflects very small delays
 2) the computational expense of trying to learn over a range of delays is very high
3) that we evolved from reflexive organisms, with short sensation->motor delays

If a law of particle physics is that event A always followed by B, but with a delay of exactly 500 hours, would we have discovered it yet?

I think not.
1
Artem Kaznatcheev's profile photo
 
I think we could get 500 hours, our upper limit is a delay of length-of-typical-PhD-program.
Add a comment...

Alex Holcombe

Shared publicly  - 
 
Peter Suber, in a recent interview (http://lj.libraryjournal.com/2015/09/opinion/not-dead-yet/an-interview-with-peter-suber-on-open-access-not-dead-yet/#_), said that more than 2,000 formerly-subscription journals have converted to full open access, and many more are considering how.  I had never heard before that the number was so large.  With two thousand instances, there is the potential for an incredible database of know-how on both the technical and legal practicalities for each field, and the arguments needed to convince editors.   Fortunately Suber's office is working on a review of the various pathways that were used.  What we also really need to know is how the academics were convinced to do it in each case! The usual passivity of senior academics on this issue is one of the biggest obstacles.

SCOAP (the project converting all particle physics journals from subscription to open access) came up. "It has succeeded in bringing all the stakeholder organizations together, including the labs doing the research, the publishers that publish the results, and the libraries that pay for the publications", ready to switch from paying for subscriptions to paying for a grand OA deal. According to Suber, "It’s the first attempt to convert all journals in a field to OA, and there’s good reason to think it could work in other fields as well".
2
Add a comment...

Alex Holcombe

Shared publicly  - 
 
The reproducibility problem is being solved by non-journal innovations, e.g. OSF, PubPeer, the Winnower, JoVE; there are many, but each may have a role. For example, our Psychfiledrawer.org website passed 0.5 million page views. No one thinks it is the solution, yet still it has significantly helped on certain topics. 
2
1
Claudia W. Scholz's profile photo
Add a comment...

Alex Holcombe

Shared publicly  - 
1
1
Michael Bach's profile photo
 
Thanks Alex:
I had already wondered about the (to me) cryptic JOV announcement. So another journal, once borne from community (and mainly 1 person's as far as I know) activity goes down the commercial drain… Your phrase “… copyright is complicated. Researchers don’t have time to learn all this stuff.” is absolutely to the point. I couldn't agree more! Due to your explanation, I'm a little less totally ignorant now.
Thanks, bwm.
Add a comment...

Alex Holcombe

Shared publicly  - 
 
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.
4
Add a comment...

Alex Holcombe

Shared publicly  - 
 
 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
2
Dani Linares's profile photoAnna Ma-Wyatt's profile photo
2 comments
 
Thanks for sharing! That looks really useful.
Add a comment...
People
Have him in circles
1,023 people
Hai Kou Zhen's profile photo
Antonio Kabeluchi's profile photo
Eva Sands's profile photo
David T. Walker's profile photo
MBBS ADMISSION Radiant Education Consultants's profile photo
Matt Patten's profile photo
Anthony Barnhart's profile photo
Richard Kidd's profile photo
Steve Hughes's profile photo
Collections Alex is following
Education
  • Harvard University
    Psychology, 1995 - 2000
  • University of Virginia
    Cognitive Science, Psychology, 1991 - 1995
Basic Information
Gender
Male
Story
Tagline
Academic. Doing basic psychology and perception research; facilitating improvements to system of science.
Introduction
Work
Employment
  • University of Sydney
    Associate Professor, present
Places
Map of the places this user has livedMap of the places this user has livedMap of the places this user has lived
Currently
Sydney