Emacs and Sage

I have been unhappy with my current practice of cut and pasting statistical results etc. from MATLAB or Python output into LaTeX for publishing. Changes to code and recalculations lead to an endless possibility for error. So I have been working on using SageTex as an interface LaTeX. As a small step that might be helpful to others by adding the commands at the end of this post to my .emacs file (actually I use Aquamacs) I can type C-c C-c sage to run Sage on the appropriate segments of my LaTeX file (see SageTeX) for more detail. I will post in future about my experience using SageTeX for getting closer to the goal of reproducible research (SageTeX also has a MATLAB interface so I plan to use it for interfacing with MATLAB too).

;; SageTeX setup
;; This adds the command sage when in LaTeX mode (to invoke type C-C C-c sage)
(eval-after-load "tex"
'(setq TeX-command-list
(append TeX-command-list
(list
(list "sage" "sage %s.sage" 'TeX-run-command nil t :help "Run SAGE on the SAGE file corresponding to this LaTeX file (run latex first).")))))

Publication: Natural scene statistics and the structure of orientation maps in the visual cortex.

Hunt, J.J., Giacomantonio, C.E., Tang, H., Mortimer, D., Jaffer, S.,Vorobyov, V., Ericksson, G., Sengpiel, F. & Goodhill, G.J. (2009).
Natural scene statistics and the structure of orientation maps in the visual cortex.
Neuroimage, in press.

Publication: On the simulation of enzymatic digest patterns: the fragmentation of oligomeric and polymeric galacturonides by endo-polygalacturonase II

Hunt, J. J., Cameron, R. G., Williams, M. A. K. (2006)
On the simulation of enzymatic digest patterns: the fragmentation of oligomeric and polymeric galacturonides by endo-polygalacturonase II,
Biochimica et Biophysica Acta 1760:1696-1703

Access article via DOI link 10.1016/j.bbagen.2006.08.022,Local PDF, Arvix Preprint physics/0609004

Electronic publishing and the narrowing of science and scholarship

A recent publication in Science by James Evans came the intriguing conclusion that:

... ironically... one of the chief values of print library research is poor indexing. Poor indexing - indexing by titles and authors, primarily within core journals- likely had unintended consequences that assisted the integration of science and scholarship. By drawing researchers through unrelated articles, print browsing and perusal may have faciliated broader comparisons and led researchers into the past. Modern graduate education parallels this shift in publication - shorter in years, more specialized in scope, culminating less frequently in a true dissertation than an album of articles.

The move to online science appears to represent one more step on the path initiated by the much earlier shift from the contextualized monograph, like Newton's Principia or Darwin's Origin of Species, to the modern research article. The Principia and Origin, each produced over the course of more than a decade, not only were engaged in current debates, but wove their propositions into conversation with astronomers, geometers, and naturalists from centuries past. As 21st-century scientists and scholars use online searching and hyperlinking to frame and publish their arguments more efficiently, they weave them into a more focused- and more narrow-past and present.

I will derive

This might prove a useful diversion if I ever end up teaching Calc 101.



(Was recently on Slashdot)

Change blindness

Yesterday, my co-supervisor Jason Mattingley gave an excellent summary of the role of attention in human visual processing. He showed a couple of excellent clips.






Does this really occur in real life? Yes

And not included in his talk, but another interesting demonstration of change blindness in real life with some explanation about what it teaches us about attention is here.

On being sane in insane places

I recently came across the Rosenhan study (Science, 1973, 179:250-258 - see Wikipedia summary). This was an attempt to quantify type I and II errors in diagnosing mental illnesses. But it also exposed the stigma we attach to mental disorders and the inhumanity of many mental institutions.

It is clear that we cannot distinguish the sane from the insane in psychiatric hospitals. The hospital itself imposes a special environment in which the meanings of behavior can easily be misunderstood. The consequences to patients hospitalized in such an environment-the powerlessness, depersonalization, segregation, mortification, and self-labeling-seem undoubtedly countertherapeutic. I do not, even now, understand this problem well enough to perceive solutions. But two matters seem to have some promise. The first concerns the proliferation of community mental health facilities, of crisis intervention centers, of the human potential movement, and of behavior therapies that, for all of their own problems, tend to avoid psychiatric labels, to focus on specific problems and behaviors, and to retain the individual in a relatively non-pejorative environment. Clearly, to the extent that we refrain from sending the distressed to insane places, our impressions of them are less likely to be distorted. (The risk of distorted perceptions, it seems to me, is always present, since we are much more sensitive to an individual's behaviors and verbalizations than we are to the subtle contextual stimuli that often promote them. At issue here is a matter of magnitude. And, as I have shown, the magnitude of distortion is exceedingly high in the extreme context that is a psychiatric hospital.) The second matter that might prove promising speaks to the need to increase the sensitivity of mental health workers and researchers to the Catch 22 position of psychiatric patients. Simply reading materials in this area will be of help to some such workers and researchers. For others, directly experiencing the impact of psychiatric hospitalization will be of enormous use. Clearly, further research into the social psychology of such total institutions will both facilitate treatment and deepen understanding. I and the other pseudopatients in the psychiatric setting had distinctly negative reactions. We do not pretend to describe the subjective experiences of true patients. Theirs may be different from ours, particularly with the passage of time and the necessary process of adaptation to one's environment. But we can and do speak to the relatively more objective indices of treatment within the hospital. It could be a mistake, and a very unfortunate one, to consider that what happened to us derived from malice or stupidity on the part of the staff. Quite the contrary, our overwhelming impression of them was of people who really cared, who were committed and who were uncommonly intelligent. Where they failed, as they sometimes did painfully, it would be more accurate to attribute those failures to the environment in which they, too, found themselves than to personal callousness. Their perceptions and behavior were controlled by the situation, rather than being motivated by a malicious disposition. In a more benign environment, one that was less attached to global diagnosis, their behaviors and judgments might have been more benign and effective.