Introducing BMC MicroPub – fast, granular and revolutionary

(Caution: Satire ahead)

I am happy to be able to share some exciting science publishing news with you. As you know, in the past few years, there has been a tremendous progress in open access publishing. The author-paying model has been shown to be viable in large part thanks to the pioneering efforts of BMC and PLOS. In particular PLOS One has been an incredible scientific and business success story that many others are trying to copy. Although these efforts are a great step forward they don't do enough to set all of the scientific knowledge free in a timely fashion. Sure you can publish almost anything today such as metadata, datasets, negative results and the occasional scientific advancement but the publishing process still takes too much time. In addition we are forced to build a story around the bits and pieces in some laborious effort to communicate our findings in a coherent fashion. Many of us feel that this publishing format is outdated and does not fit our modern quick-paced  internet age. What I am sharing with you today is going to change that.

Introducing BMC MicroPub
In coordination with BMC we are going to launch soon the pilot phase of a new online-only publishing platform. It was though from the ground up to allow for the immediate publishing of granular scientific information. Peer-review happens after online publication of the content and evaluation is not going to be based on trivial and outdated notions of scientific impact. Best of all, it is tightly integrated with the social tools we already use today. In fact, authors are asked to register to the system with their twitter account and to link it to an ORCID author ID. From then on, their twitter feed is parsed and any tweet containing the #micropub tag will be considered a submission. Authors are themselves reviewers and any submission that gets re-tweeted by at least 3 other MicroPub registered scientists is considered to be “peer-reviewed” and a DOI is issued for that content. An author can create a longer communication by replying to a previous #micropub tweet and in this way create a chain that the journal can track and group in MicroPub stacks (TM). What the team involved here has done is nothing short of amazing. We are taking the same platform we use to share cute pictures of cats and revolutionizing scientific publishing. To start using the journal authors pay a one time registration fee followed by a modest publication charge for each published content. However, the journals is waving any charges for the first 100 authors and the first 100 publications. We hit a snag in discussions with Pubmed but with your support we will be tracked by them starting next year.

Pioneering granularity
The project started a few months ago after a first attempt I covered in a previous blog post. Right now we have also an exciting experiment in granular sharing of genome content underway. You can follow the tweets of @GenomeTweet to get an idea of the future of this brave new world. The current front page of the journal gives you an indication of some of the cool science being published by early adopters. The site is currently only available to beta-testers so here is screen-shot of the current version:

I sat down with the open access advocate Dr Mark Izen from UC Merced to discuss the new journal.

Dear Mark, given your enthusiasm for open access what do you think of this initiative?
I think that experimentation in scientific publishing is fantastic. Any attempt to promote open access and get rid of the current established closed access, impact factor driven system is a great thing. One concern I have is that, although the content is published under a CC0 license, the publishing process is currently reliant on Twitter which is a closed proprietary technology. We should really ask ourselves if this goes all the way in terms of open science.

Some would say that they don't have time to read science with this level of granularity so devoid of any significant advances. In the words of an anonymous tenured prof: “You must be joking right!?”. What would you say to these naysayers?
To be blunt, I think they lack vision. Ultimately we owe it to all tax payers to be as transparent as possible about our publicly funded science. Now we can do that, 140 characters at a time. Moreover, the possibility to drive science forward by making information available as quickly as possible is an amazing possibility. Scientists are already using twitter to share information, we are just going one step forward here and going to start sharing science as it happens. You could get corrections on your protocol before your experiments have finished running ! If you blink your eyes you may literally lose the next big discovery.

So you are not concerned that this increasing level of granularity, small bite research, is going to drown everyone in noise and actually slow down the spread of information in science ? 
Absolutely not. It is a filter failure and we are sure that someone is bound to come up with a solution. In the future all sorts of different signals will allow us to filter through all this content and weed out the most interesting parts for you. You will be able to get to your computer and get in your email or in some website just the information that an algorithm thinks you should read. I am sure it is doable, it is question of setting it up.


Disclaimer: If you have not noticed by now, this is a fictional post meant to entertain. 

@World

(caution, fiction ahead)


I wake up in the middle of the night startled by some noise. Pulse racing I try to focus my attention outwards. Something breaking, glass shattering? Is someone out there ? I reach out with my senses but an awkward feeling nags at me, bubbling up to my consciousness. I try hard to focus, it is coming from outside the room , someone is inside my house. I close my eyes but vertigo takes over and weightlessness empowers me. I am in the living room cleaning the floor, picking up a broken glass. The nagging feeling finally assaults me fully. I am moving but I am not in control. Panic rises quickly as I watch helpless the simple and quiet actions of someone else. I stop picking up glass and I feel curious, only it is not exactly me, the feeling is there besides me.
- Hi, who are you ?
The voice catches me by surprise and my fear goes beyond rational control. All I can think of is to escape. to go away from here. For a second time I find myself floating as if searching for a way out. When I open my eyes again I am by the beach and I breath a sigh of relief. The constant sound of the waves calms me down for a few seconds until my eyes start drifting to the side. No, stay there I am in control! I look into the eyes of a total stranger that smiles back at me in recognition. Two voices ask me if I am enjoying the view and I can only scream back in confusion.

I wake up in the middle of the night startled by some noise. I immediately flex my hands in front of my eyes to make sure it was nothing but a nightmare trying hard to calm down. What a dream. I get up and check on the noise coming from the living room realizing that it was just the storm outside. Feeling better I fire up my laptop and grab a glass of water from the kitchen. I open twitter and type away:
- I had the strangest dream !(cursor blinking) Our senses were all connected(enter)
I get up to open the window drinking another sip of water. After a couple of steps I feel a jabbing headache forcing me to stop and bright spots of light blur my vision. I close my eyes in pain and the voices of some unseen crowd thunder in my ears:
- I had the same dream - the all say in unison
The sound of glass shattering on the floor in the last thing I remember before collapsing.

I wake up in the middle of the night startled by some noise (...)

(Twistori was the main motivation for this post)

Previous fiction:
The Fortune Cookie Genome

The Fortune Cookie Genome

*in an imaginary future*

Today is the day I get the sequencing results back. It is going be interesting to have finally a glimpse of my very own genome. At the same time I am afraid of the potential disease associations they might find in there. In any case I rather know it with time to do something about it. Thats it ... I exhale and open the main door to the building walking up the desk.

- Hi. I have an appointment with my genetic adviser.
- Oh yes, go up to the 3rd floor, they are expecting you.

I walk up a DNA shaped stairway and walk into the office of one of the attending specialists. He was the one convincing me of how useful it would be to purchase the GenomeSurvey(TM) package.

- I got your email. The results are in ?
- Yes, we have your genome fully sequenced and uploaded into your service of choice. I see you have picked Google Health as your storage provider as part of the package.
- Is there any bad news ? Will I have a serious disease soon ?
- I understand your concern. There is really nothing too serious, but I will come to that in moment. You may login with your Google account here and I can guide you through some of the results.

I login to my health page and I am confronted with the usual simple white-blue Google interface. I noticed the addition of a genome tab and let my adviser tell me more about it.

- As you can see, your genome as been uploaded to your account. It has also been submitted as an John Doe genome to the NCBI personal genomics database. You may select later to make your identity known and/or associate any of your personal history information to it.
- What about the disease associations ?
- Yes. So you can click here on the associations report to have a full listings of the phenotypic associations. You have a very healthy genome, no serious rare diseases. In your case the most important finding is that you have a 2% increased likelihood of developing a heart condition when you are above 60 and a 1% increased likelihood of having Alzeimer's disease after 65.
- That's it ? 2% ? 1 %?
- Well, that is assuming no prior knowledge on your diet and other personal history as established in the large HapMap version 10. From now on you may input into the forms provided in Google Health all your diet and other personal information on a daily basis and as the information accumulates the service will automatically update the probabilities. As your adviser I should tell you that this information can be used by Google to provide you with better targeted advertisement in all other Google products.
- Right ... is this it ? Does the package include anything else ?
- Of course ! As I mentioned to you before you can click here on the prescription tab to get an informal advice on how best to deal with the associations that were found for you. You should always discuss these suggestions with your doctor before doing anything. By company policy I cannot read this information with you, since we are not liable for this. You can read it at home when you get there.
- Well , if there is nothing else I will go.
- Thank you again for choosing our GenomeSurvey(TM) package I am happy to have served you and I hope that you feel more empowered about your own health. Be well.

I go home feeling a bit cheated but obviously happy of having no serious disorder in the horizon. I rush to my home computer to read the prescription that will help me prevent my heart condition and Alzeimers. I click the GoolgeDoctor(TM) button and a clip like avatar jumps around in the screen. A computerized voice reads aloud the text appearing in the screen:

Dear Pedro. You can call me clipy ! I will be your assistant for any of your health needs. In order to decrease the likelihood for the negative phenotypes associated to your genome please consider abiding by the following rules:
- Do a lot of exercise
- Eat a healthy diet
- Find balance in your life

*in an imaginary present*

- Snap out of it, what does your say ?
I look back to the small piece of paper in my hand and read:
- "You must find balance in your life", thats what it says.
- Well, these things are never wrong.

I drop the paper on my dish and finish eating the fortune cookie before leaving the chinese restaurant with my friends.
- You won't believe what I thought of ...

Further reading
The Future of Personal Genomics (21 September 2007 Science)
How much information is there really in personal genomes and how much should patients know ? Extra points for citing a post from Eye on Dna in a Science Policy Forum.
The Science and Business of Genetic Ancestry Testing (10th October 2007 Science)
A discussion surrounding results of genetic ancestry tests and the commercialization of these tests.
Google Says Its Health Platform Is Due In Early 2008 (17 October InformationWeek)
Google is still trying to build a platform to host the health related information. Microsoft already launched a service called HealthVault (read about it from Deepak).
BMC Medical Genomics (17 October BMC blog)
BMC will launch a journal dedicated to Medical Genomics, covering articles on "on functional genomics, genome structure, genome-scale population genetics, epigenomics, proteomics, systems analysis and pharmacogenomics in relation to human health and disease."
Do-it-yourself science (17 October Nature)
This editorial links up several news, opinions and articles in the last issue of Nature to ask the question - How much involvement can patient advocates have in genetics? The most impressive articles is the story of Hugh Rienhoff, a trained geneticist and biotechnology that decided to personally research about his daughter's disease (as in buying a PCR machine etc). (via Keith)
Common sense for our genomes (18 October Nature)
Steven E. Brenner explains the need for a Genome Commons. See discussion at bbgm.