The 2007 Impact Factors were published yesterday by Thompson Reuters.

The Impact Factor of Molecular Systems Biology for 2007 is 9.954

This represents a substantial increase over last year's Impact Factor (see chart) and we would like to warmly thank all our authors and reviewers who have contributed to this success. We will continue to work very hard to maintain the high standards of the journal and promote innovative and insightful research in systems biology.

The significance of Impact Factors suffers from intrinsic limitations (see Ian's post) and interpretation of this metric is subject to much discussion (Rossner et al 2007, Thompson's Citation Impact Forum). These and other questions related to bibliometrics are also currently debated at the Nature Network Citation in Science group.

In a nice post at bbgm, Deepak writes:

...historical online literature lacks the relevant structure and metadata to make our task easier, but it is time that publishers thought ahead about some of the advantages of online publishing.

I can't agree more. I heard sometimes the claim that within 5-10 years, more than 95% of the scientific literature is going to be read by computers only. Possible. However, the converse alternative might be interesting to consider: what if 95% of scientific papers could be 'written' by computers? Even if this formulation is obviously provocative and unrealistic, the point is that harnessing the 'network effect' of the web may have two complementary components, one community- the other computer-driven. On one hand, web 2.0 functionalities enable community-driven commenting, rating and even writing of scientific publications. On the other hand, semantic web technologies are expected to facilitate computer-driven integration of scientific data from multiple sources, which is likely to play an increasingly important role in science. Rather than mining thousands of unread papers, the scientist of the future may rather search the web for relevant data first and integrate it to generate – or 'write' – novel insight. In fact, integration of large datasets already represents a major field of research in systems biology (see Chuang et al 2007, Xue et al 2007 or Mani et al 2008 as recent examples published in Mol Syst Biol).

It seems thus that, in addition of being web 2.0 enabled, new publishing models should 'embed' more structured data into online publications. In short, 'papers' could progressively transform into hybrid online objects that resemble more to database records (see Timo Hannay's post on this topic) or highly structured documents. At the extreme, one could even imagine to publish 'naked' datasets, without any 'stories' around them. Of course, efficient data integration will require the data to be in a standard and structured format and its quality will have to be well characterized. These are all far from trivial qualities.

The good old-fashioned papers are probably not going to disappear as publication units, in particular for high-impact studies reporting novel and deep insights. It is also not the point here to propose dumping every scientist's hard drive into the web. Data-rich publications would be published only when the authors would feel it appropriate. There might thus be some equilibrium to find between papers that will never be read except by a text mining engine and pure datasets, published as a resource, easier to search, to mine and to integrate. This dialectic may ultimately boil down to the issue of how well will text mining and data integration technologies perform in the future.

In any case, within the context of the current debate about the saturation of the peer-review system, I wonder whether a data-centric form of scientific publishing could help to release somewhat the pressure. Reviewing of datasets might be quicker and could rely more on standardized evaluation parameters. If assorted with proper credit attribution mechanisms and metrics of impact, data-rich (or even data-only) publications may represent an alternative model complementing the traditional 'paper' format. It would prevent the loss of useful data otherwise buried in verbal descriptions and, most importantly, would hopefully stimulate web-wide integration of disparate datasets.

Here is the answer provided by Kevin Struhl in an interesting interview published a few days ago in Current Biology (Current Biology 2008 18:R7):

"I think it is flawed at several levels. Anonymous reviews assume that reviewers are unbiased, objective and without personal or scientific conflicts of interest; this is not always true, especially in competitive situations, and there is no mechanism to detect such problems. Aside from the potential for abuse, anonymous reviews create an inequality between authors and reviewers that is unfair and scientifically unjustified. At many journals, particularly those run by commercial companies as opposed to scientific societies, disagreements between authors and reviewers are often adjudicated by editors with modest scientific accomplishments and experience. I favor a process in which editorial decisions are made by practising scientific experts, reviewers are identified by name, and the signed reviews and author responses published online along with the paper. Lastly, it is unfortunate that the biology community has permitted commercial companies to control most of the journals. Competition among journals and business-related decisions about scientific publishing has seriously distorted the literature, and it has created an artificial rating system that is used to judge decisions about funding and career advancement."

Following adoption of a new publication licence (see below) we have now also updated our instructions to authors to clarify our guidelines on the availability of published material, data and software, and, last but not least, redesigned the look & feel of our website to make it visually more attractive, to integrate the blog directly in our home page and to provide a retrospective look of the top PDF downloads of papers published in Molecular Systems Biology.

Come and visit us, the papers are cool!

The text below is an adaptation of a Correspondence submitted to PLoS Biology on October 22 and published October 31 as a "Reader Response" linked to the Editorial “When Is Open Access Not Open Access?”, (MacCallum, 2007)

I am pleased to announce that Molecular Systems Biology has changed its license to publish for all articles accepted after October 1st, 2007 (see updated instruction to authors). The new license allows our authors to choose between two Creative Commons licenses: one that allows the work to be adapted by users (by-nc-sa), the other that does not allow the work to be modified (by-nc-nd). The first articles to be published under the new license are expected to appear online beginning of next month.

Our content is therefore not only freely available to all but our authors can now also decide to make their research fully open for reuse and adaptations.

The current explosive development of data and text mining, semantic-web and information aggregation technologies is profoundly changing the publishing landscape (eg Tim O'Reilly visits Nature). When we were contacted a few months ago by the OpenWetWare community who envisaged the "wikification" of one of our Reviews (see post), we decided that Molecular Systems Biology should strongly support such initiatives by providing our content in an as open form as possible. Our Senior Editors fully supported this transition to a more open license but also encouraged us to allow authors to have some influence on the decision.

Providing authors the possibility to choose their license has some decisive advantages: first, by enforcing a conscious choice by authors it will inevitably raise awareness on the implications of the various publication licenses; second we would like to see the question of "what should be open access" being addressed in a more democratic way by the community itself rather than through incantations of what the ideal solution should be. My guess – and my personal hope – is that most of the authors will indeed choose the most open version of the license, but I think that it is important to respect the opinions of those who think differently and who would feel uncomfortable with the idea that their article can be remixed or adapted without them being aware of it.

Our attitude is motivated by the fact that, at Molecular Systems Biology, we see the role of a scientific journal more as a catalyst facilitating and accelerating scientific discovery rather than a policy-making instrument. What is Systems Biology? Rather than providing a rigid definition of a rapidly evolving field, we prefer to let the community define the scope of this field and we adapt to it. What is open access? Rather than relying on a dogmatic position in a still fluid situation, we prefer to let scientists define their priorities.

Note: To avoid confusion, I initially wanted to make this announcement only after the first paper published under the new license (that is, accepted after Oct 1st) had appeared online, but a recent Editorial from PLoS Biology (“When Is Open Access Not Open Access?” MacCallum, 2007) forced me to anticipate a little on this. In this Editorial, Catriona MacCallum reviews in details the subtleties of publishing licenses and clarifies their implications for the concept of “open access”. Unfortunately, this Editorial, at the time of its publication (Oct 16), included also erroneous information on Molecular Systems Biology, given that we had updated our policy already on Ocober 1st. In any case, it is somewhat ironic that MacCallum chose to stigmatize Molecular Systems Biology as an example of a journal that “promulgates” confusion about open access. As it turns out, Molecular Systems Biology is dedicated to the concept of making research freely available and to engage authors themselves in decisions that would achieve this goal with their own research. It is in this spirit of openness and respect for authors that we have recently adapted our license to publish.

(via Corie Lok's Blog)

There is an interesting forum on Nature Network discussing peer-reviewing and the editorial process:

Hosted by the editors of Nature Network, this group/forum is for scientists who want to learn more about scientific publishing straight from the editors of Nature and the other Nature journals. Join the group and post your questions in the forum. We’ll do our best to get the right editor to answer them here. (Ask the Nature Editor)

It is an interesting timing, because EMBO is currently hosting a PhD course (The EMBO Young Investigator PhD course) that provides students with tutorials and practical exercises on peer-reviewing. On Sunday, the students had a lecture by Karim Labib on how to write a referee report; I gave yesterday a presentation (here on Google doc) on scientific publishing and the editorial process; today, the EMBO Journal editors sit together with the attendees to discuss referee reports written by the students on a series of "test cases".

I have discussed previously some of the problems associated with peer-reviewing (The Good, the Bad and the Ugly) and I believe that this types of initiatives--PhD courses, direct contact with editors--raise awareness of the importance of having an efficient editorial/peer-reviewing process in science and represent concrete and constructive ways to improve the present situation.

EMBO publishes The EMBO Journal, EMBO Reports and is co-owner with Nature Publishing Group of Molecular Systems Biology. In view of the great success of these three journals (and the associated increasing workload...), the editorial team at EMBO will be expanded.

Two positions as full time scientific editor are open. From the ad (read full job description):

Candidates should have a strong scientific background, a PhD and preferably some post-doctoral experience. They should have a broad interest in diverse areas of the life sciences, with a thorough knowledge of molecular biology. For Molecular Systems Biology, experience or strong interest in systems biology and related area, are required.

Closing date: 23.09.2007

An editorial office can sometimes appear like a mysterious black box and you may ask: why should I apply there? What is so great about being an editor? Everyone has a different opinion, but for me it is definitely to be continuously exposed to the latest advances in research across the entire breadth of the discipline and to be involved in scientific discussions at a very high level with our authors, editorial board members and reviewers. Take Molecular Systems Biology: a new journal in an emerging discipline. Of course, I might be a little biased ;-) but it is hard for me to imagine a more exciting and privileged position. For an insider's view of the Molecular Systems Biology editorial office, I recommend reading the post from Pedro who spent a few months with us as a trainee.

What do we do? Most of our time is devoted to reading (entirely!) submitted manuscripts and the associated literature, seeking reviewers (time-consuming!) and making decisions (delicate!). These core activities place the editor at the heart of the scientific process and therefore, the job comes with its respective level of responsibility. We are of course guided and supported by our Advisory Editorial Board, Senior Editors and reviewers, but making a final decision is a crucial aspect of this job.

What about creativity? It is true that the critical reading of manuscripts needs more analytical thinking, a sense for synthesis, and, to enjoy it, unlimited curiosity, than scientific creativity. But a journal needs also to be developed, content has to be commissioned and new links and partnerships with the relevant scientific communities have to be developed. Moreover, the world of scientific publishing is currently in mutation, almost in ebullition, and faces challenges that will require the most dynamic and innovative minds. New types of quantitative, structured, and/or large scale data play an increasingly important role in molecular biology, calling for definitions of new standards and novel ways of communicating, archiving and retrieving scientific knowledge. On the publishing side, the roles of authors, reviewers and publishers are progressively redefined by increasingly large collaborative structures (see discussions here and here), different publication models ('publish-then-filter') and web 2.0 technologies (eg Open science or Amazon: a new kind of publisher).

For sure, as in every job, there are downsides and exchanges between editors and authors are sometimes robust. Researchers may storm at editorial rejections and lousy referee reports and editors will be pestered by appeals (Unappealing situation) and ... lousy referee reports (The Good, the Bad and the Ugly). However, beyond these inevitable frictions, which require their good dose of diplomacy, it is important to remember, as Pernille Rorth writes,

that scientists, in turn, act as authors, reviewers and editors, and thus 'wear different hats' in the process. (Authors, reviewers and editors at The EMBO Journal, Rorth, 2005).

In conclusion, for those who like constant intellectual challenge, professional responsibilities and love the unpredictable diversity of science, I encourage you to apply to the positions above!

Nature Genetics publishes this month an Editorial ("Compete, collaborate, compel") on how to provide incentives and credit to authors who deposit data in public repositories--so called procedures for "microattribution". The idea is to include at the end of papers a complete list of accession codes identifying all the data used in the study. To provide incentive to data producers, a ranking of the most used accessions could be published, generating a measure of the impact of cited database records. Clearly, such an initiative would require "heroic structural solution at the journal level".

The issue of finding adequate incentives and credit mechanisms for datasets relates to the increasingly intimate relationship between scientific publishing and databases:

the dividing line between the two realms is getting ever fuzzier, and may eventually disappear altogether. As journals have moved online, they have taken on some of the characteristics of databases (searchable, structured, constantly updated). Meanwhile, some databases are starting to mimic certain aspects of journals (peer-reviewed, archival, citable). This has led to the appearance of 'hybrid' publication that are both databases and journals depending on how you look at them (Foo and beyond, Timo Hannay, 2007).

One might wonder whether the idea cannot be pushed even one step further and think of merging the concepts of publication, database and computational model into a single entity (a Document, Record and Model, a DReaM...?). In fact, several initiatives in this direction have already been started (see for example YeastPheromoneModel.org, The Center for the Development of a Virtual Tumor). Publishing services could eventually provide something like a "Publishing Integrated Development Environment", by analogy with IDEs available for software development, with the option to open new projects integrating progressively various contributions using strict identification and control version systems. Different types of credit would go to those initiating a project and providing the necessary initial components and to those contributing, incrementally, to the development of the project. "Presubmission" inquiries would be evaluated to grant potential authors access to the necessary resources (computational or experimental) of the project, which may represent an additional incentive for participation. Upon analysis and interpretation of the results, individual contributions, including data, model, results and documentation, would be "published" in the project after adequate peer-reviewing to ensure strict quality control. These contributions would be uniquely identified and citable. Perhaps some form of "sensitivity analysis" could even provide an instantaneous measure of the impact and relevance of a contribution.

Such a "DReaM" system would certainly not replace good old-fashioned papers, but would rather live in parallel. Its function would be to structure research around important topics by providing a framework for coherent efforts directed to common goals and to facilitate "microattribution" mechanisms not only for data producers but also for modelers.

This is a quick reminder of this year's partnership between Molecular Systems Biology and the International Conference for Systems Biology 2007. From the submission page:

Extended abstracts submitted by July 27, 2007 will be evaluated by a committee consisting of ICSB reviewers. Authors of selected abstracts will be invited to submit full manuscripts for possible publication in Molecular Systems Biology. A special issue of Molecular Systems Biology devoted to ICSB 2007 will be published online in March/April 2008. The full manuscripts will go through the standard review procedure of the journal, but if accepted, the publication fees (USD $3000) will be paid by ICSB 2007.

Deadline for submission of extended abstracts: tomorrow, July 27th, 2007!

For the fun of it, here are a few examples of definitions:

To understand complex biological systems requires the integration of experimental and computational research -- in other words a systems biology approach. (Kitano, 2002)

Systems biology studies biological systems by systematically perturbing them (biologically, genetically, or chemically); monitoring the gene, protein, and informational pathway responses; integrating these data; and ultimately, formulating mathematical models that describe the structure of the system and its response to individual perturbations. (Ideker et al, 2001)

[...]the objective of systems biology [can be] defined as the understanding of network behavior, and in particular their dynamic aspects, which requires the utilization of methematical modeling tightly linked to experiment. (Cassman, 2005)

By discovering how function arises in dynamic interactions, systems biology addresses the missing links between molecules and physiology. Top-down systems biology identifies molecular interaction networks on the basis of correlated molecular behavior observed in genome-wide "omics" studies. Bottom-up systems biology examines the mechanisms through which functional properties arise in the interactions of known components. (Bruggeman and Westerhoff, 2007)

Why is it so difficult to come up with a concise definition of systems biology? One of the reasons might be that every definition has to respect a delicate balance between "the yin and the yang" of the discipline: the integration of experimental and computational approaches (Kitano, 2002); the balance between genome-wide systematical approaches (Ideker et al, 2001) and smaller-scale quantitative studies (Tyson et al, 2001); top-down versus bottom-up strategies to solve systems architecture and functional properties (Bruggeman and Westerhoff, 2007). But despite the diversity in opinions and views, there might be two main aspects that are conserved across these definitions: a) a system-level approach attempts to consider all the components of a system; b) the properties and interactions of the components are linked with functions performed by the intact system via a computational model. This may in fact reveal another source of difficulty when trying to define systems biology, which is to find a general and objective definition of "biological function" (or Lander's "goal of the system", see our brief post Teleology and Systems Biology). Feel free to comment and suggest on this...

In any case, rather than trying too hard to draw conceptual boundaries with theoretical definitions, I thought it would be interesting to see how the field defines itself. I introduced all the original research articles published in Molecular Systems Biology into del.icio.us and tagged the entries to have an idea of the distribution of several aspects of the research we publish. Inevitably my tags have rather broad meanings and the boundaries are often fuzzy (eg what is a "mechanism"?), but I tried my best by taking into account the following dimensions:

• scale of the study: genenome-wide vs small scale or single-cell, etc
• biological approach: transcriptomics, proteomics etc...
• computational approach: simulation, data-driven correlation model, network structural model, etc...
• insight gained: dynamics of the system, global properties (modularity, robustness, evolvability...), mechanistic insight, etc...

Here is the result, as a "tag cloud"

There is a clear, and not too surprising, dominance of genome-wide 'omics'-type of studies (in particular transcriptomics). But it is also good to see that the small-scale studies, often using quantitative approaches and focusing on systems dynamics are also well represented. Again, this classification is very crude and somewhat arbitrary, but it provides nevertheless, at a glance, an overview of the landscape of systems biology. If I find the time, I will try to refine the concepts and introduce our content in a more structured way into freebase. Finding a structured way to characterize the "insight" of a study might be particularly challenging but it could be an instructive exercise.

Molecular Systems Biology received its first impact factor: 7.941 !

This impact factor refers to citations accumulated in 2006 for papers published in 2005. The journal was launched in March 2005 and is visible in MEDLINE since June 2006. This is obviously an "early" impact factor, but it already shows the dynamism of the field. This is great news not only for the journal but also for the community.

Here is a small comparative table of some journals with related or overlapping scopes:

The Royal Society seeks your views on the emerging area of synthetic biology. This is your opportunity to shape the focus of the Royal Society's policy future work in this important area. We welcome views from individuals or organisations by 27 August 2007.

• Potential developments and applications
• Current research capacity and geographical distribution
• Societal implications
• Ethical concerns
• Biosecurity risks
• Implications for the environment
• Research support and funding
• Implications for human health
• Legal issues and implications for regulation (national and international)
• Ownership, sharing and innovation frameworks (including intellectual property)
• Biosafety concerns
• Education and training
• Governance and oversight of research
• Economic considerations for developed and developing countries

Nature Precedings, the new free pre-publication server from NPG, is now live (see Nascent, Editorial, Pedro). I just had a first look at the content and was more than pleased to see that items relevant to systems biology have already been posted. The category bioinformatics is the most represented so far.

To facilitate monitoring of systems biology related submissions to Nature Precedings, I have now added a tab "Precedings" to our Quick links on the left sidebar (the feed is constructed via this yahoo pipe).

A few weeks ago, we published a series of articles (Edwards NJ, Feala et al, Lu et al, McCord et al, Shlomi et al, Ulitsky and Shamir, Zhou X et al, 2007) that were initially presented at the RECOMB Workshop on Systems Biology . According to the publication model agreed upon, peer-reviewed articles were presented orally at the conference and a subset of those were invited for revision and ultimately published in Molecular Systems Biology. Publication of research paper at a conference is very popular in computer sciences and bioinformatics, but it is a rarely applied model in biology (Ideker et al, 2007).

I see several several major incentives for this type of collaboration between a conference and a journal, particularly for an emerging field like systems biology. First, it may help the journal to stay more in sync with a rapidly evolving community. Second, it may well stimulate presentation of novel and exciting research at the conference (and perhaps reduce somewhat the proportion of talks reporting only previously published data...). Finally, the proximity in time between public presentation, direct discussion with peers and ultimately publication in a journal may accelerate the dissemination of results and increase the pace of the field.

We wish now to extend this joint conference/journal presentation model by entering a collaboration this year with the International Conference for Systems Biology, to be held in Long Beach, California, from October 1-6, 2007. Authors of the best abstracts from the conference will be invited to submit the corresponding research articles to Molecular Systems Biology. Manuscripts will go through the standard review procedure of the journal, but if accepted, the publication fees will be paid by ICSB 2007. A special online issue of Molecular Systems Biology devoted to ICSB 2007 will feature the accepted articles.

More information on the precise procedure on the abstract submission page of the Conference. Deadline for submission of the abstracts: July 27th, 2007!

(via Kaiser-J 2007, Science 316:529 and discuss [AT] syntheticbiology.org)

The National Science Advisory Board for Biosecurity (NSABB) has released a Draft Report (available as pdf) providing recommendations on how to minimize misuse of biological research. This report was discussed publicly on April 19, 2007 (see webcast).

The 50-page draft makes it clear that there is a difficult dialectic between imposing restrictions on research that can be misused for harmful purposes on one hand, and, on the other hand, the necessity of facilitating open and rapid information exchange to accelerate scientific progress, for the benefit of society in general, but also to precisely counteract potential threats. The report insists on the prime importance of openness in scientific research and clearly states that unrestricted progress and communication should be the "default position".

One major recommendation of the draft report is that Principal Investigators should carry the responsibility for the initial evaluation of the potential for misuse of their own research. Concrete implementations could be inclusion of check boxes in grant proposal forms and annual reports to the researchers institution to formally certify that risk assessment has been performed.

Dual Use Research of Concern is defined as follows:

Research that, based on current understanding, can be reasonably anticipated to provide knowledge, products, or technologies that could be directly misapplied by others to pose a threat to public health and safety, agriculture, plants, animals, the environment, or material.

To aid identification of research that might be qualified as "dual use research of concern", seven categories are listed (inspired from the National Research Council "experiments of concerns", in Biotechnology Research in an Age of Terrorism):

1. Enhance the harmful consequences of a biological agent or toxin.
2. Disrupt immunity or the effectiveness of an immunization without clinical and/or agricultural justification
3. Confer to a biological agent or toxin, resistance to clinically and/or agriculturally useful prophylactic or therapeutic interventions against that agent or toxin, or facilitate their ability to evade detection methodologies.
4. Increase the stability , transmissibility, or the ability to disseminate a biological agent or toxin.
5. Alter the host range or tropism of a biological agent or toxin.
6. Enhance the susceptibility of a host population.
7. Generate a novel pathogenic agent or toxin, or reconstitute an eradicated or extinct biological agent.

The philosophy of self-regulation by researchers appears to be in line with the stated purposes of raising awareness on dual use research issues and promoting a culture of responsibility within the scientific community. The report recognizes however major difficulties in defining a threshold at which dual use research would be clearly "of concern", which makes it difficult to come up with clearcut and concrete recommendations. In the report, NSABB provides "tools" to assist the formulation of an appropriately balanced response via a risk/benefit assessment in research management and communication. The final decision will influence content, timing and distribution of publications reporting "dual use" research. As such, scientific journals will play an important role in developing a "Code of Conduct for Dual Use Research in the Life Sciences":

Those who play decision-making roles in the process of communicating scientific information have an ethical responsibility to consider whether the information being considered for publication could be used to endanger public health, agriculture, plants, animals, the environment, or materiel. Depending on their analysis of the risks and benefits of communications regarding information or technology that meet criteria for dual use research of concern, they may choose to proceed in a way that mitigates or manages the risks associated with communication – for example, by adding contextual information not found in the original article, or delaying communication until a time at which the risks would be reduced.

1. What entity should be in charge of reviewing research identified by PIs as dual use of concern?
2. Is the definition of dual use research of concern appropriate in terms of its "specificity" and "sensitivity"?
3. Are the listed seven categories of potentially dual use research appropriate?
4. Should the PI be the sole and prime responsible to identify his own research as dual use of concern?
5. What additional guidance is required?
6. What burden does these recommendations (eg necessity to review research identified as dual use of concern) represent for your institution?

see also:
Statement on the consideration of biodefence and biosecurity (2003) Nature 421:771
Nature journals' policy on biosecurity
BIODEFENSE: Proposed Biosecurity Review Plan Endorses Self-Regulation. Kaiser-J (2007), Science 316:529
Will Bioterror Fears Spawn Science Censorship? Granick-J (2007) Wired

In a correspondence addressed to PLoS Biology, entitled "An Incentive Solution to the Peer review Problem", Marc Hauser and Ernst Fehr propose that editors should punish slow reviewers. The proposed "incentive solution"? Deliberately delaying submissions from slow or bad reviewers! "You were two weeks late with your report? I am going to sit on your manuscript for four..."

It is rather difficult to articulate what sort of violation to the editorial principles this would actually represent! Even if I am willing to accept that the proposal is half a joke and half a provocation, its purely coercive nature strikes me - in fact it even hurts. It is clear that when scientists accept to review a manuscript–and do so for free, when they are most of the time submerged by traveling, teaching and administrative duties– it is certainly not because editors are pointing a gun to their chest. There must be some positive motivations: could it be a sense of duty, scientific interest and intellectual stimulation to critically analyze a study, desire to stay updated on the latest advances in the field?

Here we go: the Molecular Systems Biology blog is launched, at last! I hope you will like it and react to it. Rather than providing theoretical goals or formal definitions, I finally decided to leave online some entries I posted prior to the launch, in order to give a flavor of the scope and style of this blog. Let's see how it will evolve, depending also on your feedback and suggestions.

I would also like to take the opportunity to warmly thank Pedro Beltrao (Public Rambling) for his invaluable help setting up the blog.

Welcome again and, please enter, the door is open!

by George M Church, Senior Editor

Image manipulation and selective reporting of images have been recently in the focus of a healthy debate on the issue of scientific data manipulation. Of course, as editors tell us how they detect fakes ("What's in a picture? The temptation of image manipulation", Rossner and Yamada, JCB 2004 166:11), there is a danger that authors will be tempted to upgrade their ploys. More importantly, I think that these issues are symptomatic of a much larger problem in Cell & Molecular Biology which is the lack of protocols for getting from raw data to conclusions. Contrast this with genomics and 3D-structural biology where raw data are available in databases, not just a few typical photos, but every scrap of data (e.g. sequence trace data, diffraction intensities, raw RNA array data). The algorithms for getting to the conclusions are public and other labs are encouraged to redo the trajectories from data to conclusions using the original or new algorithms. This is mostly missing from Cell & Molecular Biology papers, with some excuse like "too expensive". Maybe it’s too expensive NOT to do it – not just because of data faking, but because it sends the message that we’re too lazy (or too busy) to describe in detail how we do our science and how to systematically improve it.

Molecular Systems Biology would like to encourage anyone who has creative and concrete ideas how to get Molecular and Cell Biology up to the standards of genomics and structural biology.