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Reproducibility: A tragedy of errors : Nature News & Comment http://www.nature.com/news/reproducibility-a-tragedy-of-errors-1.19264

 

Happy New Year to you!

RE: Your blog vs. G+, what if I told you that you might have your cake and eat it too? I too have a WordPress blog, but I've tacked a few bits on to the back end and this allows me to use my blog as the primary hub for my work as you're suggesting you plan on doing. I then use platforms (walled silos) like Google+, Twitter, and Facebook to syndicate my material out to allow for a broader reach by leveraging social networks effects to my benefit. Even better, I've got things set up so that comments on platforms like Google+ feed back to my blog, which allows me to not only live on my own site, but it also allows me to "own" all of the content and commentary that's generated from it. (This way if Google+ is shut down next month, I'd still have all of the generated commentary, which could live indefinitely on my own site.) Thus your followers who prefer to read your material on other platforms (G+, in your case) aren't left without the content you're generating, but their commentary also appears back on the blog to add to the larger conversation.

First, consider using the "Jetpack" module (free software built by the same company that makes WordPress) and its publicize functionality to connect your G+ account and auto-post (syndicate) your Azimuth content automatically to G+. (This also frees up a good bit of time to not have to do it manually.) If nothing else, this will help to keep some of your audience engaged.

Second, to port the comments from the syndicated G+ post back to your original post on Azimuth (comments from G+ will show up as comments in WordPress that you can approve/delete just like other WP comments; this also prevents you from spending so much time in G+ after you turn off comment notifications) you can follow the details at the IndieWebCamp site (http://indiewebcamp.com/Getting_Started_on_WordPress) to add/configure a few simple plugins as well as to connect http://brid.gy to allow social networks to communicate with your blog.

If you need help/assistance to make the technical hurdles a bit lower, I'm happy to help walk you through the details or even do it for you (gratis) if you'd like. All of the modules I've mentioned are free and open source and under very active development.

For a simple example see the comments on this post http://boffosocko.com/2014/07/05/the-mnemonic-major-system-and-gregg-shorthand-have-the-same-underlying-structure/#comment-27045 which originated from G+
https://plus.google.com/+ChrisAldrich1/posts/ZfvtRPmwhtj

For a brief overview, you might appreciate the opening few paragraphs of http://indiewebcamp.com/.

 

.@NatureNews Why can't I use my own @Disqus account to comment on your site instead of a new one you've made for me?

 

My reply to ‘Novel, amazing, innovative’: positive words on the rise in science papers | Nature News & Comment
http://www.nature.com/news/novel-amazing-innovative-positive-words-on-the-rise-in-science-papers-1.19024

I can readily posit a potential and very strong motivation for the uptick in the appearance of these words, and particularly for the word "novel", which the paper and this article fail to see.

Beginning in the early 90's, and certainly starting before that time, there has been an intensified interest for both research institutions and researchers writing papers for them to monetize their research outside the halls of the academy. (Particularly with decreased funding for faculty and intensified competition for research dollars - many research faculty either self-fund their salaries or rely heavily on 3rd party income.) Toward this end, individual researchers began more aggressively pursuing patents for their research work and at the institutional level, colleges and universities began very actively pursuing technology transfer to the point of opening up full offices and hiring large numbers of staff to better leverage the return of creating patents and pursuing sales and licensing deals for the resulting research work. The US Patent Office, in making a determination of whether or not to grant patents, (and even moreso when the underlying documents are published scientific research articles) uses words like "novel" and "innovative" as an indicator of their worthiness. Without a patent, it's incredibly difficult to protect the intellectual property contained within a published and public work. Other words like "amazing" which are also cited in the paper are geared (in a business sales sense) more toward potential corporate financial investors who may consider purchasing or licensing the resulting work of a research paper. What corporate bean counter wants to invest in a dull-sounding research paper title which is quite likely one of the only parts of the document they're likely to comprehend? Yet throw in some "excitement words" and you may have a sale!

When one looks at employment contracts of the professoriate (post-docs, graduate students, and the like), which presumably comprises the majority of those publishing papers with these words, one will see that professors prior to the 90's have contracts that don't mention intellectual property rights resulting from their efforts, or which grant them the lion's share. Current contracts after that period will almost necessarily keep either all or most of these types of revenue streams in the institution's pockets rather than the researchers themselves. I'd be willing to bet that this tide began turning in the mid-1970s and has certainly been overwhelming since the mid-90s.

It is these severe economic taskmasters which are almost assuredly the cause of the rise of these buzzwords in research papers, and most particularly in their titles. One need only ask themselves, which university wants to be the next proverbial "Stanford" to not have a piece of revenue from the intellectual property of a proverbial "Page rank" algorithm? Or in biomedical research, to not take a hefty cut out of a drug which could potentially cure cancer or HIV/AIDS? Take a gander at what something as simple as a HELA cell, which was taken and cultured without any notice to Henrietta Lacks, has become from an industrial perspective. If they can avoid it, academia certainly won't let multi-million (or billion) dollar enterprises spring up (again) without them receiving a piece of the pie.

Naturally, there are other factors compounding the issues at hand, particularly when one looks at negative research findings, which are sadly rarely ever published, particularly in an era of big data when what we know isn't true will surely help assist in defining the boundaries of what we do know and what could potentially be determined at that boundary. (Much the way that white space in photographs or in printed pages helps to define an image as much if not more so than the darker portions of the image.) Negative words are likely more difficult to get published as it may reflect poorly on researchers who are reliant on continued future funding and may see their sources disappear when they're not producing groundbreaking work. My hypothesis, however, is that it's more likely a direct economic impact based on technology transfer than it is the increased competitive landscape in academic research.

 

[1406.1391] ";A Vehicle of Symbols and Nothing More."; George Romanes, Theory of Mind, Information, and Samuel Butler

Donald Forsdyke indicates [at https://www.quantamagazine.org/20151119-life-is-information-adami/#comment-361734] that "...Polymath Adami has "looked at so many fields of science" and has correctly indicated the underlying importance of information theory, to which he has made important contributions. However, perhaps because the interview was concerned with the origin of life and was edited and condensed, many readers may get the impression that IT is only a few decades old. However, information ideas in biology can be traced back to at least 19th century sources. In the 1870s Ewald Hering in Prague and Samuel Butler in London laid the foundations. Butler's work was later taken up by Richard Semon in Munich, whose writings inspired the young Erwin Schrodinger in the early decades of the 20th century. The emergence of his text – "What is Life" – from Dublin in the 1940s, inspired those who gave us DNA structure and the associated information concepts in "the classic period" of molecular biology. For more please see: Forsdyke, D. R. (2015) History of Psychiatry 26 (3), 270-287."

Let's look into this and see where, if at all, there may be a bridge over to either Claude Shannon or Boolean Algebra.

 

@fadesingh, While I do agree in part with your comment that the technical side of the math could have been explored a bit more, to me, part of what this story is highlighting (and to great benefit as well) is the "other" personal side of mathematics which is rarely seen by the broader public. Most of math and math history is full of seemingly brilliant solo (read: lone wolf) researchers developing mathematics de novo in dark, smoke and caffeine-filled rooms and emerging with iron clad proofs. This particular story shows the growing more collaborative and friendly side of math in addition to the years of slow development of friendships and theory which have culminated into something potentially interesting. I would suggest that in this case you not take them too hard to task on the subject, particularly as the article was being written contemporaneously with the publication of the journal article itself. (The article here was published <i>just</i> in advance of the arXiv post, such that it didn't even include the link to the paper itself, though it was added the following day.)

I love that Quanta is continually exploring the areas of math and science at the depth and level which they've become accustomed. They're filling a very important gap in science communication between technical journal articles and somewhat sophisticated outlets like National Geographic, Scientific American, and Wired (in which they are also distributed, but yet are still an editorial cut above comparatively. [Cross reference: <a href="http://stream.boffosocko.com/2015/evolution-of-a-scientific-journal-article-title-from-nature-to">Evolution of a Scientific Journal Article Title (from Nature to TMZ)</a>] I'm sure that C.P. Snow himself would praise them for helping to close the gap between the "Two Cultures."

 

While I'm positive that stories about math at the level of sophistication described here require some technical underpinning which the writer and editors may potentially lack and which therefore make it both more difficult to be aware of them (to know to report on them in the first place) but also to objectively lay out the topic, from a journalistic perspective, this particular story, which references prior work by Benedict Gross, should have at least mentioned, as a caveat, the relationship between Quanta as a publisher and Gross's position as an advisory board member to it.

While Gross's bona fides are certainly not in question given the topic or his distinguished career, what, if any, was his involvement with the piece? Did he suggest it? Did he provide background? (I notice he wasn't directly quoted, which makes me wonder even further). Was he paid? There's certainly the possibility that something potentially not quite kosher may be going on here (even if it is just free publicity for him and his past work, particularly given that the final result discussed here hasn't been published or independently verified), and not providing at least a mention of the relationship from an editorial standpoint is a glaring error.

Aside from this small journalistic oversight, I otherwise laud Quanta for consistently providing interesting, entertaining, and timely coverage of the world of math and science in such a fantastic fashion. Helping to humanize and even idolize mathematicians and scientists should be a more common effort in our society.

Given the somewhat broad nature of the readership and range of backgrounds, for those who may not have the high level of background for reading the related papers (once they're publicly available) yet, many may be interested in knowing that Dr. Gross has an excellent and free online series of lectures on basic abstract algebra available (http://www.extension.harvard.edu/open-learning-initiative/abstract-algebra) which may go a reasonable part of the way for helping the not-so-technical readers to better understand some of these areas of mathematics and how they interrelate.

Cross posted as: https://www.quantamagazine.org/20151208-four-mathematicians/#comment-363094


 

@wheelissa Other part wants to chastise them for lack of civility & make crude double entendre comment about in academe

 

Replied to a post on github.com :

Sorry for the delay, but my work schedule and travel have been awfully heavy lately. It does sound like the issue I'm having is somewhat related to the discussion on https://github.com/raamdev/independent-publisher/issues/155

I've got two separate installs with the same IndieWeb plugins installed. One uses Independent Publisher and the other is a slightly older version of the Academica Theme (v1.2.3 downloadable from https://www.dropbox.com/sh/ym0c78uyzltpeu1/AAByejNd8MG83I2MVOFXOuPaa?dl=0) which is outputting the facebook likes, twitter favorites, and reposts properly (or at least as I would expect.)

For some reason Independent Publisher isn't outputting Brid.gy likes, favorites, or resahares from Twitter and Facebook out of the box the way that Academica (or even WP common themes like Twenty Fourteen or Twenty Fifteen) does. They're not showing up at all. On the site with Academica Theme, I've tried doing a "Live Preview" of the Independent Publisher theme and there, it also seems to be "eating" (not showing) these additional comments from Brid.gy while all the other traditional comments do show up.

However, while you're tracking down the issue(s), you might also consider tweaking one additional output issue with respect to these types of comments. From a UI standpoint for themes using IndieWeb, I would recommend that the comment section sort out the comments and display them somewhat differently. For simple Facebook likes and Twitter favorites, it might be best to aggregate all of them into a facepile [http://indiewebcamp.com/facepile] with a simple header ("Liked on Facebook"/"Favorited on Twitter") followed by the photo icons of the people who liked/favorited the article within those platforms. (This is similar to how most Wordpress sites handle Likes/Stars natively within WordPress.) Following this it could create a facepile of people who reposted/reshared the post. Then after this the rest of the comments should be sorted by date/time as comments traditionally are as this will allow people to more easily read/consume the actual commentary.

This post has an example of a combination of likes/favorites/reposts and actual comments that would be better sorted into a facepile section followed by a more "traditional" comments section. http://boffosocko.com/2015/07/27/algebraic-number-theory-ucla-extension/

I'm supposing that it's how Independent Publisher is rendering the output of wp_commentmeta into its comment section that causes some of these brid.gy-fed likes/favorites/reposts to disappear.

If it helps, I'll also point out a previous and possibly related issue I'd run across vis-a-vis IndieWeb and output of comments: https://github.com/pfefferle/wordpress-webmention-for-comments/issues/1. The solution was most likely the way that the Semantic Linkbacks plugin (an IndieWeb WP-specific plugin) was handling its output. Here it's likely that @dshanske or pfefferle may be of more assistance in sorting things out if necessary.

 

Johns Hopkins adopts statement on academic freedom principles, philosophy | Hub

to come back to Moulton's comment here on tenure faculty versus other levels. Check to see how the tenure ratio fits into rankings of universities and colleges.

 

I'm still attempting to understand the larger world of indieweb code for WP, but I'm relatively sure that the issue I'm seeing is potentially coming out of the WP Semantic-Linkbacks plugin.

The issue:
Likes from Facebook as well as likes and RT's from Facebook are feeding into the the WP comments dashboard from brid.gy properly, but once being approved, aren't actually showing up in the comments section of the related WP post.
I've done a quick test with a comment with text on the same Facebook post and don't seem to be seeing the same issue and it seems to show up fine in the comments on the post once approved.

Example:
WP post: <a href="http://lfl8424.boffosocko.com/2015/08/20/todays-books-august-20-2015/">http://lfl8424.boffosocko.com/2015/08/20/todays-books-august-20-2015/</a>;
Associated facebook post: <a href="https://www.facebook.com/ChrisAldrich/posts/10100846770831315">https://www.facebook.com/ChrisAldrich/posts/10100846770831315</a>;

As this is a relatively new site, perhaps there's some small thing that I'm missing or forgetting? I set it all up with the WP IndieWeb plugin (v2.2.0) and everything within it is current and installed/configured (except Hum and Micropub).

Its possible that it's something similar to a related issue I'd had before on a different WP install (see: https://github.com/pfefferle/wordpress-webmention-for-comments/issues/1) though that seemed to be fixed (by itself?) shortly thereafter.

Within the WP admin interface, (http://lfl8424.boffosocko.com/wp-admin/comment.php?action=editcomment&c=25)
in the editable comment section, I'm seeing something similar to the following:

<code><a href="http://lfl8424.boffosocko.com/2015/08/20/todays-books-august-20-2015" rel="nofollow"></a>
<a href="http://lfl8424.boffosocko.com/2015/08/20/todays-books-august-20-2015/" rel="nofollow"></a></code>

So there is data there, it's just not being parsed/rendered properly somewhere.

Since I've got another WP set up that seems to be operating properly with the same general set up, has anyone got any ideas?

 

Thanks Bobby, but that exactly the same method I mentioned in the comment just above yours on June 15 and alluded to in my question to you yesterday. Sadly, it takes too many clicks for something that should be easily available or that should actually even include embedable functionality like almost any other social network. LinkedIn should provide an easier way of finding the URL directly.

 

I like what you've done with the final product and have always thought about doing something similar myself, particularly after I saw what Martin Fenner (https://plus.google.com/106537123721037364937/posts) did with his site at http://blog.martinfenner.org/ which actually allows others to make changes to it via github. Naturally, I'm also highly interested in his take on scholarly communication too, which makes me want to delve in there even more.

Another thing I've been playing around with lately has been some tools/toys at http://indiewebcamp.com primarily within WordPress (I noticed you had one at http://teaching.proftalbert.com/, so you're at least somewhat familiar) though also a bit with http://withknown.com which is a platform built specifically with education in mind (https://withknown.com/education/).

A large part of their philosophy is to own one's own data and then syndicate it out to other social media/external site, but some of their infrastructure allows one to easily make posts on one's own page which then act as replies on another's site. This is particularly interesting from the viewpoint of teaching wherein students and professors can interact with each other, but still have/own all of their individual work. (Incidentally, it also makes for using one's own site as a commonplace book of sorts, which I often find valuable.)

As an exmple, you'll notice on the post on my blog http://boffosocko.com/2015/05/21/category-theory-anyone/ got automatically syndicated to Google+ the other day. Then you replied to it within Google+ but my site sucked your comment back into the comments section on my original blog post, thereby keeping the conversation on my site and not only just on Google's.

 

Along with @JHAA_President I hope all @JHU_Alumni comment on this statement of academic freedom. http://list.alumni.jhu.edu/read/archive?id=2121492&mid=25550973&e=chrisaldrich%40jhu%2eedu&x=3963e34b

For bonus points, can you find the repeated sentence and the glaring repeated error I saw? http://web.jhu.edu/administration/provost/initiatives/academicfreedom/

Some of my thoughts on academic freedom can be found here: http://boffosocko.com/2014/04/22/reframing-what-academic-freedom-means-in-the-ditigal-age/

 

A Comment on the Academica Wordpress Theme

2 min read

In reply to: https://wordpress.org/support/topic/surprised-by-all-the-bad-reviews

I agree wholeheartedly with Adam, though I don't think I'd really seen any small issues except perhaps for an odd CSS issue in formatting an h2 tag somewhere. (Note: This comment applies to v1.2.3 of Academica as on 4/2/15, the theme publisher made a DRASTIC change to the theme, so take caution in upgrading!!)

I have created a child-theme with one or two small customizations (slightly larger headings in side widgets and some color/text size changes), but otherwise have v1.2.3 working as perfectly as it was intended to. This includes the slideshow functionality on the homepage. See BoffoSocko as an example.

For those, perhaps including Adam, wanting to get the slider to work properly:

  • Go to your WP Dashboard hover on the menu tab "appearance" and click on "customize"
  • On the "Featured Content" tab, enter a tag you want to use to feature content on the homepage of your site. (In my case, I chose "featured" and also clicked "Hide tag from displaying in post meta and tag clouds".)
  • Go to one or more posts (I think it works on up to 10 featurable posts) and tag them with the word you just used in the featured content setting (in my case "featured"
  • Next be sure to actually set a "Featured photo" for the post--930x300 pixels is the optimal photo size if I recall.
  • Now when you visit your home page, the slider should work properly and include arrows to scroll through them (these aren't as obvious on featured photos with white backgrounds).
  • Note that on individual pages, you'll still have static header image(s) which are also customizable in the "customize" section of the WP dashboard, which was mentioned in step 1.

I hope this helps.