Cretaceous African ant in amber (Courtesy of Vincent Perrichot via http://myrmecos.wordpress.com)

1. A peer-review paper gets published;
2. The media gets hold on the story;
3. The blogs react: scientists and general public fill the comments section (in the genuine tone of the internets);
4. The authors of the original paper join in the discussion.

Discussion may get heated, comments may get bitter, but the results are always rewarding for all.

Most people in academia will cringe at the thought of formally citing a page that exists only on the internets. One main objection is that the electronic information could not be there the next time one tries to access it. This is what has kept the ICZN from allowing publication of new species names in online peer-reviewed journals, even well established ones.

In reality formal citation of electronic media has become more common than scientists realize. In systematics, for example, many of the specialized software we use is distributed directly by the authors (who are research biologists themselves), and URLs to the pages where these applications can be downloaded are included as part of the citation. Many electronic databases accessible through the web, like antbase.org and antweb.org for myrmecology, have accumulated multiple formal citations in recent years. And if that doesn’t convince you just think about the ubiquity of GenBank– after all, a list of GenBank accession numbers is nothing but the digital identifiers of information about particular pieces of genetic information stored on an database that is accessible online.

Pers. comm. to me is the right comparison for a blog post (at least the type of posts I write): part of the content is original unpublished information; part is word of mouth circulating within the scientific community; part is published information. Above all, it is the blogger’s subjective opinion on a topic. But most importantly for citation purposes, blog posts are not peer-reviewed material. As long as people bear this in mind, I see referring to a blog post as a legitimate practice equivalent to pers. comm. There is a significant difference, however. By providing an URL the author (the editor) allows anyone who so wishes to check the original source for further details. As such, a blog citation serves as an enhanced pers. comm.

A sign of the (slowly rising) acceptance of blogging in academic circles is the inclusion of standards on how to cite electronic media in style manuals. As with printed media, there are now many acceptable ways to cite a blog post, varying from journal to journal. Citing this post can be done as following:

Keller, R. A. (2009) Citing blogs in scientific papers. [Weblog.] Archetype. May 27. (http://roberto.kellerperez.com/2009/05/citing-blogs-on-scientific-papers/). Date accessed.

And my recent post on the clypeus would be,

Keller, R. A. (2009) Homology Weekly: Clypeus. [Weblog.] Archetype. May 22. (http://roberto.kellerperez.com/2009/05/homology-weekly-clypeus/). May 27 2009.

Now, all the journals I want to keep track off offer TOCs e-mail alerts or RSS feeds but one: Zootaxa. This journal not only moves fast as part of its editorial policy but also publishes a lot of papers on ants. I was growing so annoyed by not having a RSS feed for this journal that a couple of weeks ago I contacted chief editor Zhi-Qiang Zhang to demand beg suggest such service. His kind reply was that they know they need to do it, they don’t know how to do it, and their staff is currently so loaded with publishing work that they don’t have the time to do it. But he would welcome any suggestions.

I, unfortunately, don’t know how to implemented this either, but cybertaxonomist Rod Page from the University of Glasgow does. He just set up a page where you can subscribe to a RSS feed for Zootaxa for your taxon of interest.

The timing was coincidence– he just happens to be working on some projects that need such feeds. If you follow iPhylo or any of Page’s blogs you know it took him one coffee break to build.

Thank you Rod.

A spruced-up version of a dirty box mite. 2009 © DEWalter.

A new blog just sprung into life. Macromite’s Blog:

This blog will be devoted to mites and mite art. My original Mite Image
Gallery was hosted by the University of Queensland until I left there
in 2003. Since then it has been lying dormant on a variety of computers
in a much colder land. Many of my images continue to be available on
the web (e.g. in interactive keys) and, if you are fortunate enough to
live in Australia, you may have seen some of them at the recent
Ornamentamology exhibit created by the Jewellers and Metalsmiths Group
Queensland, but amazingly, there doesn’t seem to be a site devoted to
appreciating the often bizarre beauty of the Acari. Now there is.

This person puts me to a shame when it comes to enhancing and coloring images from scanning electron microscopy (SEM). I rarely ever mask the background out, for example, mainly because it is a pain even for simple, bare contours. I can’t imagine the work that went into masking each of those hairs on the legs and the feather-like hairs on the body to produce the image above (from this post). Notice how the true cuticle of the mite’s body peeks at varous points in salmon color through the light pink of the covering dirt, requiring a lot of masking work also.

It is not all post-production, however. Having worked extensively with scanning electron microscopy I can tell you that, giving the quality of the original images he starts with (sometimes a full set just for a single final image), there was already a lot of work in both specimen preparation and flight-hours at the microscope.

And if I stop drooling over my keyboard from looking at the images and read the text on each post, I may even learn something about mite taxonomy.

Each session was more or less arranged around controversial topics and the organizers made an effort to include people across disciplines- there were biologists, philosophers, anthropologists, linguists and even the odd economist. The latter is working on applying a Darwinian framework to study the evolution of political institutions, but appears to have a hard time convincing his peers that Darwinian evolutionary theory does not implies teleology nor does it provides a scientific justification for racism. Good luck with that.

The highlight for me was to meet philosopher of biology John Wilkins, who keeps one of my favorite blogs at ScienceBlogs. During his talk he covered the murky and much discussed topic of species. One of the basic premises of his work is that if you take the Essentialist story seriously and set out to study all those pre-Darwinian taxonomists who believed that species had essences and were therefore unable to accommodate evolution into their worldview, you won’t find any. Not even all the way to Aristotle. It is yet more research arriving at the conclusion that Ernts Mayr constructed a straw-man of unenlightened typologists just for marketing purposes while promoting his version of the Biological Species Concept. The fruits of Wilkins decade-long research on species is about to be published in the form of two books.

I was able to harass him during coffee breaks and dinner with annoying questions about philosophy of taxonomy. He is a very clear thinker and I’m happy to report that he answered all my questions graciously. And in case you were wondering, irl he looks just like the great white gorilla in his blog’s avatar. I know, it’s freakish.

ScienceBlogs started a new blog with an interesting dynamic, the title of which is either a very clever use of terms or a super-geeky pun, depending on your level of causticity: Photo Synthesis.

The internet is home to a wealth of captivating science images, from the many microscopic components of a cell to the remote corners of the universe captured by Hubble. On Photo Synthesis, we aim to bring you the best of what’s out there. Every month we will feature the work of a different photoblogger, exposing worlds both small and large, familiar and exotic. We will let the power of the lens take us where we ourselves are not able to go.

And if the blog’s description wasn’t enough to get one’s interest, they invited no other than entomologist Alex Wild (or Alejandro Salvaje, as we known him south the USA border) as inaugural editor. He is not only an excellent researcher and blogger, but if you thought scientists abuse Gary Larson’s cartoons on their talks you should see what we do with Alex’s insect photographs.

Go check his astonishing ant sampler:

Most blogs will let people display a small image icon or avatar whenever they leave a comment in the discussion section of a post or forum. But in many sites, unless you have created an account previously (if such option exists in the first place) the avatar displayed for you will be a boring generic silhouette or a random colorful pattern (like the ones appearing on this blog). Enter Gravatar. The name stands for Globally Recognized Avatar, and what this service does is let you associate an image of your choice to the e-mail address you normally use for posting comments on blogs. The avatar image will then follow you around from blog to blog, provided the blog or forum has enable Gravatars (most blog applications now do). It is a centralized avatar repository.

Creating a Gravatar is very simple: just signup, upload the image of your choice, and define which e-mail address(es) you want that image to be associated with. That’s it. Your e-mail address will not be used for anything else. No spam.

I, for example, can go and harass Alex Wild at Myrmecos Blog with my less-than-insightful comments and he will always have to deal with my green ant Gravatar made from a SEM image of Oecophylla smaragdina (Fabricius).

A side note. If you don’t have a blog, you should know that bloggers will appreciate comments by readers no matter how small or simply they are (the comments that is).

The reviewer writes:

Lessig argues that a strict divide between the world of sharing and the world of commerce is counterproductive. He wants to refocus attention away from the stalemated copyright wars and towards a more vibrant ‘read–write culture’ that remixes rather than replaces what came before.

[...]

In Remix, he outlines the case for licences that make one’s work free for non-commercial use but reserve any right to commercial exploitation to the author — something that is traditionally anathema to the free-software movement.

In general, Lessig centers his arguments around debates that are of interests to a wide audience, like the ones surrounding the music industry and web-portals like YouTube. The issue of copyright is, however, of importance for science as well since it impacts the way scientific knowledge is disseminated and shared. An example in the realm of myrmecology concerns the taxonomic literature dealing with species descriptions that is stored in antbase.org: as of today, you can freely access all the taxonomic works produced on this group of insects since 1758 with the exception of the most recent ones, as they are protected by copyright laws.

In my view, you have to look no further for a prime example of the benefits of a read-write cultural than the practice of science itself, hence my interest in how the Science Commons projects develops.

The book is now in my (already long) reading list. You can (freely) access the review in full at Nature’s’ website:

How to end the copyright wars. Jonathan Zittrain reviews Remix: Making Art and Commerce Thrive in the Hybrid Economy by Lawrence Lessig. Nature 457, 264-265 (15 January 2009) | doi:10.1038/457264a.

Science Commons designs strategies and tools for faster, more efficient web-enabled scientific research. We identify unnecessary barriers to research, craft policy guidelines and legal agreements to lower those barriers, and develop technology to make research, data and materials easier to find and use.

Our goal is to speed the translation of data into discovery — unlocking the value of research so more people can benefit from the work scientists are doing.

They just released a short video about this initiative.