A Blog Around The Clock

i-710d005c8660d36282911838843a792d-ClockWeb logo2.JPGA post from December 5, 2007:


Communication of any kind, including communication of empirical information about the world (which includes scientific information), is constrained by three factors: technology, social factors, and, as a special case of social factors – official conventions. The term “constrained” I used above has two meanings – one negative, one positive. In a negative meaning, a constraint imposes limits and makes certain directions less likely, more difficult or impossible. In its positive meaning, constraint means that some directions are easy and obvious and thus much more likely for everyone to go to. Different technological and societal constraints shape what and how is communicated at different times in history and in different places on Earth.

Technology – Most communication throughout history, including today, is oral communication, constrained by human language, cognitive capabilities and physical distance. Oral communication today, in contrast to early history, is more likely to include a larger number of people in the audience with whom the speaker is not personally acquanted. It may also include technologies for distance transmission of sound, e.g., telephone or podcasts. This is the most “natural” means of communication.

Smoke signals and tom-toms introduced new constraints to communication – the messages had to be codified, short and simple and much of verbal and non-verbal communication had to be eliminated. Invention of writing, on stone tablets, clay tablets and papyrus, and later on paper and in print, changed the constraints further, making some aspects of communication easier and others more difficult, leading to the development of universal rules and norms of written communication. Unlike oral communication, the written communication is unidirectional, from one to many, making feedback from the audience difficult or impossible. Thus, it is necessarily linear. Its permanence also requires greater care be taken about the form and content. Finally, physical constraints (i.e., the size of a book) impose a structure to written communication, e.g., breaking down the work into chapters, subheadings and paragraphs, placed in a particular order. Also, written communication introduces the concept of authorship (and readership) while oral communication is “owned” by all the participants in the conversation.

Society – What and how is communicated differs dramatically if the audience is small and familiar (e.g., one’s children or neighbors) or large and unfamiliar (speaking at a conference). Written communication is, by definition, aimed at a large and unfamiliar audience, which has an effect on form, style and content of communication. Local habits and traditions further determine the forms and styles of communication.

Conventions – Different types of communication within particular groups of people are often officially codified, often precisely defining the language, style and format. Legal and scientific literature are probably the most extreme examples of a very strict code imposed by official societies. Such strict formalization of communication was initially very useful, imposing order (positive meaning of “constraint”) to an otherwise chaotic and undependable mish-mash of communication forms, allowing all the members of the community to understand and trust each other. However, when such strict forms last for decades and centuries, they are often made out-dated by the passage of time, invention of new technologies and societal changes, thus making the negative meaning of ‘constraint’ more and more obvious.

Scientific Communication

Development of communication of science reflects the development of science itself. Communication of information about the facts about the world did not differ much from other forms of communication for most of history until science itself started distinguishing itself as a special type of human endeavor, different from philosophy and religion. The way science communication evolved parallels the changes in our thinking about the scientific method. At the time when trips to the countryside and armchair thinking were still regarded as science, much of communication was in the form of books. When the hypothetico-deductive aspect of the scientific method “won” as the scientific method, the fledgling scientific societies, led by the Royal Society in the UK and the Academy in France, designed the form and structure of the scientific paper – the form we still use today: title, author, abstract, introduction, materials and methods, results, discussion and references.

Today, we understand that the hypothetico-deductive method is just one of several elements of the scientific method (see this) and that the standard format of the scientific paper is perfectly unsuitable for publication of findings reached through other methods.

Description of new species (extant or extinct) requires a monograph format, for which specialized journals exist that cater to this particular format. Ecological surveys are often straight-jacketed into the standard format, with addition of unwarranted mathematization – not all science requires numbers and statistics. Finally, science is getting more and more collaborative – single-author papers are becoming a rarity, while the papers boasting 10, 20, 50 or even 100 authors are becoming a norm, which challenges the way authorship in science is determined (see this and links within).

But what really made the limitations of the standard format obvious is the genomic revolution. Sequencing a genome is not hypothetico-deductive science – it is akin to an ecological survey: apply a technique and see what you get! Now that the excitement of publication of the first few genomes has receded, the existing journals are inadequate platforms for publication of new genomes. While sequencing is getting easier with time, it is still expensive and time-consuming. Yet, the techniques have been standardized and there is really not much to say in the introduction, materials and methods or discussion sections of a genome paper. All that is needed is a place to deposit the raw data as tools for future research in an easily-minable format that makes such future research easy. The data would be accompanied by the minimal additional information: which species (or individual) was sequenced, which standard method was used (and if it was modified), and who did the work. It is not, any more, an intellectually creative endeavor, as useful as it is for the progress of biology and medicine.

Science On The Web

When e-mail first became popular as a communication method, some people understood it as an extension of the written communication (letters) while others took it to be a new form of oral communication (telephone). Of course, it is both and more. Two people can rapidly exchange a large number of brief personal messages (as in a phone conversation), or one can send a long e-mail message to a large group of people, written with proper grammar, capitalization, punctuation and formatting (as a pamphlet). And yet, it is also neither – unlike oral communication, there is no way to convey non-verbal communication (thus the invention of emoticons ;-) ). Unlike written communication, it is fast, informal, not usually taken very seriously or read carefully, and is easy to delete. E-mail is now a communication form of its own.

The communication on the Web is, likewise, a whole new form. Again, some people see it as written communication (putting an article or book online in order to reach more readers and nothing more), while others see it as a more personal, oral communication that is written down (and such people, unlike the first group, love podcasts and videos which add the non-verbal components of communication to the text). The former prefer static web-pages with their ‘feel’ of permanence. The latter prefer Usenet, livejournals and blogs. The latter perceive the former as stodgy, authoritarian and boring. The former perceive the latter as wild, illiterate and untrustworthy. Again, they are both right and they are both wrong – it is a whole new way of communicating, fusing and meshing the two styles in sometimes unpredictable ways – it is a mix of written and oral communication that combines permanency and authority with immediacy, honesty and the ability for rapid many-to-many communication. The younger generation will use it naturally (though this does not mean that many senior citizens today did not grasp it already as well).

So, how will the constraints (both positive and negative) imposed by the new technology and new social norms alter the formality of the scientific communication, including the format of the scientific paper?

Online, the constraints of the paper and printing press will be gone. No more need for volumes, or issues, or page numbers, or, for that matter, for the formal scientific papers.

The standard format of the scientific paper will become just one of many (and probably not the dominant or most frequent) form of scientific communication. Different people have different talents and inclinations. One is analytic, another synthetic. One is creative, another a hard worker. One has great hands with the equipment or animals, while another is good with computers and statistics. One has a lot of space and money and a network of collaborators at a prestigious institution, another is stuck in a small office somewhere in the developing world with no research funds at all. And each can make a valid and useful contribution to science. How?

One will have a great idea and publish it online. The other will turn the idea into an experimental protocol that tests the idea and will publish it somewhere online. The next will make a video of the experimental method. The next person will go to the lab and actually follow the protocol and post raw data online. The next person will take the data an analyze it and post the results somewhere else online. The next person will graph and visualize the data for easier understanding. The next person will write an essay that interprets the findings and puts them into the broader context (e.g., what does it mean?). The next one will write a summary that combines several of those findings (a review). The next will place that entire research program into the historical or philosophical context. The next will translate it into normal language that lay-people can understand.

They are all co-authors of the work. Each used his/her own strengths, knowledge and talents to contribute to the work. Yet they did not publish together, simultaneously or in the same online space, though all the pieces link to each other and thus can be accessed from a single spot. That single spot is the Scientific Journal, a place that hosts all of the pieces and links them together (also see Vernor Vinge’s vision of the science of the future, combining laboratories at universities with online boards where ideas and results are rapidly exchanged).

In the future, journals will be online hosts for all styles of scientific contribution and ways to link them together (within and betwen journals) – from hypotheses and experimental methods, to data, analyses, graphs to syntheses and philosophical discussions. The peers will review each other in real time and assign each other portions of the available funding according to the community perceptions of the individual’s needs and qualities. Universities will be places for teaching/training the next generations of scientists and for housing the labs. The PhD will be needed for becoming a professor, but not for becoming a worthy and respected contributor to science – that evaluation will be up to peers.

This may sound like science fiction, but we are already living in it. Repositories (like arXiv and Nature Precedings), science blogs, OA journals, Open Notebook Science (what Rosie Redfield and Jean-Claude Bradley do, for instance) are already here. And there is no going back.

So, how do we prepare for this future? Word: slowly but smartly. Science has some very conservative elements (in a non-political sense of the term) that will resist change. They will denigrate online contributions unless they are peer-reviewed in a traditional sense and published in a reputable journal in the traditional format of a scientific paper. Some will retire and die out. Others can be reformed. But such reforming takes patience and careful hand-holding.

The division of scientists into two camps as to understanding of the Web is obvious in the commentary on PLoS ONE articles (which is my job to monitor closely). Some scientists, usually themselves bloggers, treat the commentary space as a virtual conference – a place where real-time oral communication is written down for the sake of historical record. Their comments are short, blunt and to the point. Others write long treatises with lists of references. Even if their conclusions are negative, they are very polite about it (and very sensitive when on the receiving end of criticism). The former regard the latter as dishonest and thin-skinned. The latter see the former as rude and untrustworthy (just like in journalism). In the future, the two styles will fuse – the conversation will speed up and the comments will get shorter, but will still retain the sense of mutual respect (i.e., unlike on political blogs, nobody will be called an ‘idiot’ routinely). It is important to educate the users that the commentary space on TOPAZ-based journals is not a place for op-eds, neither it is a blog, but a record of conversations that are likely to be happening in the hallways at conferences, at lab meetings and journal clubs, preserved for posterity for the edification of students, scientists and historians of the future.

PLoS ONE is a good example of the scientific journal of the future that I have in mind – the ONE place where all the data will be deposited. The commentary space and the Hubs are where all the really interesting stuff will be happening before and after publication of data: hypotheses, methods, videos, podcasts, blogs, debates, discussions, user-user peer-review, etc. The other PLoS Journals will be places, closely connected to ONE and the Hubs, of course, where works of special value will be highlighted – high-quality, media-worthy and large/complete pieces of work, plus editorials, news, etc. – the added value. They are a necessary link between the present (past?) and the future – the showcase of the quality that we can provide and thus hopefully change the minds of the more resistant members of the scientific community.


  1. #1 Wobbler
    April 9, 2008

    Hi Coturnix,

    Interesting post (I like your user-user peer review term, I think some people refer to that as peer commentary). I am wondering what your views are on institutional repositories vs central repositories like BioMed? Stevan Harnad and co (Peter Suber, Alma Swan and the like) seem to favor institutional over centralized archiving and using OAI-PMH harvesters (like http://www.oaister.org/) to have them manageable/searchable from one central location (meta data, without the content being actually centralized).

    Apparently, this protocol is flexible enough to support peer review/ commentary/ discussions and so forth according to this site: http://wiki.cetis.ac.uk/What_is_the_OAI_Protocol_for_Metadata_Harvesting. Not sure how well that works compared to simply having these features implemented in central repositories, though.

    And while I also think the scenario you describe here is on its way and inevitable, it will take plenty of time (and probably new perspectives) still to get scholars (especially the experience/senior ones) to contribute more enthusiastically on the digital scholarly highway.

  2. #2 McDawg
    May 1, 2008

    Interesting comment Wobbler.

    Great blog you’ve got BTW.

    Whilst is may not (yet) specifically address your point, the new Open Access Directory sounds like a great place for open discussion/contribution by anyone who’s remotely interested in any of these issues.

  3. #3 Wobbler
    May 1, 2008

    Hi McDawg,

    Thanks for the kind comment *blushes*. I have read about the Open Access Directory on Peter Suber’s blog as well, but have not got the time to dive into it yet. I will check it out soon, it sounds very interesting. Thanks for the link!

  4. #4 McDawg
    May 1, 2008

    @ Wobbler ‘Nae bother’ as they say here in Scotland.

    I myself have only briefly looked at the OAD wiki. I guess it will take at least a couple of months to really get the ball rolling but I have really good feeling about it.

    With 21 OA mandates already in place with more and more to follow, a more structured deposition system will hopefully follow whether this be central, institutional or a combination of both I guess.

    It is also worth flagging up Repository 66

  5. #5 Wobbler
    May 1, 2008

    Indeed, since even ‘a journey of a thousand miles must begin with a single step’ as Lao-Tsu has said back in ancient China.

    And I believe OA has long made that first step and is firmly walking towards its goal, going all around the world. Still a long way to go and plenty of mountains to conquer, though. So good initiatives are going to help it overcome these mountains faster.