Calvin Bridges in 1935 (Photo Credit: Smithsonian Institution Collections SIA Acc. 90-105 [SIA2008-0022])

Recently, I stumbled across a listing in the New York Times for an exhibit in Brooklyn recreating the original Columbia Fly Room, which will be used as a set in an upcoming film of the same name directed by Alexis Gambis. Gambis’ film approaches the Fly Room from the perspective of a visit to the lab by one of Bridges children, Betsy Bridges. I recommend other Drosophila enthusiasts to check out The Fly Room website and follow @theflyroom and @alexisgambis on Twitter for updates about the project.

In digging around more about this project, I found a link to the Kickstarter page that was used to raise funds for the film. This page includes an amazing story about Bridges that I had never heard about previously. Apparently, after Morgan and his group moved to Caltech in 1928, Bridges built from scratch a futuristic car of his own design called “The Lightening Bug”. This initially came a big surprise to me, but on reflection it is in keeping with Bridge’s role as the main technical innovator for the original Drosophila group. For example, Bridges introduced the binocular dissecting scope, the etherizer, the controlled temperature incubator, and agar-based fly food into the Drosophilist’s toolkit.

Here is a clipping from Modern Mechanix from Aug 1936 describing the Lightening Bug:

Coverage of Calvin Bridge’s Lightning Bug in Modern Mechanix (Aug 1936).

Bridge’s Lightening Bug was notable enough to be written up in Time Magazine in May 1936, which described his car as follows:

It is almost perfectly streamlined, even the license plates and tail-lamp being recessed into the body and covered with Pyralin windows flush with the streamlining. There are no door handles; the doors must be opened with special keys. Dr. Bridges pronounced the Lightning Bug crash-proof and carbon-monoxide-proof. “My whole aim,” said he, “was to show what could be done to attain safety, economy and readability in a small car.”

Newshawks discovered that for months, when he got tired of looking at fruit flies, the geneticist had retired to a garage, put on a greasy jumper and worked on his car far into the night, hammering, welding, machining parts on a lathe. Now & then, the foreman reported, Dr. Bridges hit his thumb with a hammer. Once he had to visit a hospital to have removed some tiny bits of steel which flew into his eyes. It was Calvin Bridges’ splendid eyesight which first attracted Dr. Morgan’s interest in him when Bridges was a shaggy, enthusiastic student at Columbia.

Calvin Bridges next to the Lightening Bug (Time Magazine, 4 May 1936).

Gambis has also posted a video of the Lightening Bug being driven by Bridges taken by Pathé News. Gambis estimates this clip was from around 1938, but it is probably from 1936/7 since Bridges died in Dec 1938 and by the time Ed Novitski started graduate school at CalTech in the autumn of 1938 Bridges was terminally ill, but appears fit in this clip.  This clip clearly shows the design of Bridges’ Lightening Bug was years ahead of its time in comparison to the other cars in the background. I also would wager this is the only video footage in existence of Calvin Bridges.

The only other information I could find on the web about the Lightening Bug was a small news clipping that was making the rounds in local new April/May 1936:

Interestingly, the only mention I can find of this story in historical accounts of the Drosophila group is one parenthetical note by Shine and Wrobel in their 1976 biography of Morgan that had previously escaped my notice. On page 120, they discuss how Morgan handled the receipt of his 1933 Nobel Prize in Physiology or Medicine (emphasis mine):

…Morgan was very modest about the honor. He frequently pointed out that it was a tribute to experimental biology than to any one man….As Morgan acknowledged the joint nature of the work, he divided the tax-free $40,000 award equally among his own children and those of Bridges and Sturtevant (but not of Muller’s). He gave no reason; in the letter to Sturtevant for example, he said merely I’m enclosing some money for your children. (Bridges, however, is said to have used his to build a new car.)

So there you have it: Calvin Bridges, Drosophila geneticist, was also an unsung automotive pioneer whose foray into designing futuristic cars was likely funded in part by the proceeds of the 1933 Nobel Prize!

Related Posts:

• Modern Mechanix: Lightning Bug Car Is Crash Proof
• Kickstarter: Calvin’s Lightning Bug

Just as Scientists themselves are adopting social media, many scientific journals/magazines are as well. However, most discussions about the role of social media in scientific exchange overlook the issue of how we Scientists believe traditional media outlets, like scientific journals, should engage in this new forum. For example in the Darling et al. paper on the The Role of Twitter in the Life Cycle of a Scientific Publication, little is said about the role of journal Twitter accounts in the life cycle of publications beyond noting:

…to encourage fruitful post-publication critique and interactions, scientific journals could appoint dedicated online tweet editors who can storify and post tweets related to their papers.

This oversight is particularly noteworthy for several reasons. First, it is fact that many journals, and journal staff, play active roles in engaging with the scientific debate on social media and are not simply passive players in the new scientific landscape.  Second, Scientists need to be aware that journals extensively monitor our discussions and activity on social media in ways that were not previously possible, and we need to consider how this affects the future of scientific publishing. Third, Scientists should see social media represents an opportunity to establish new working relationships with journals that break down the old models that increasingly seem to harm both Science and Scientists.

In the same way that we Scientists are offering tips/advice to each other for how to participate in the new media, I feel that this conversation should also be extended to what we feel are best practices for journals to engage in the scientific process through social media. To kick this off, I’d like to list some do’s and don’ts for how I think journals should handle their presence on Twitter, based on my experiences following, watching and interacting with journals on Twitter over the last couple of years.

• Do engage with (and have a presence on) social media. Twitter is rapidly on the uptake with scientists, and is the perfect forum to quickly transmit/receive information to/from your author pool/readership. I find it a little strange in fact if a journal doesn’t have a Twitter account these days.
• Do establish a social media policy for your official Twitter account. Better yet, make it public, so Scientists know the scope of what we should expect from your account.
• Don’t use information from Twitter to influence editorial or production processes, such as the acceptance/rejection of papers or choice of reviewers.  This should be an explicit part of your social media policy. Information on social media could be incorrect and by using unverified information from Twitter you could allow competitors/allies to block/promote each other’s work.
• Don’t use a journal Twitter account as a table of contents for your journal. Email TOCs or RSS feeds exist for this purpose already.
• Do tweet highlights from your journal or other journals. This is actually what I am looking for in a journal Twitter account, just as I am from the accounts of other Scientists.
• Do use journal accounts to retweet unmodified comments from Scientists or other media outlets about papers in your journal. This is a good way for Scientists to find other researchers interested in a topic and know what is being said about work in your journal. But leave the original tweet intact, so we can trace it to the originator and so it doesn’t look like you have edited the sentiment to suit your interests.
• Don’t use journal account to express personal opinions. I find it totally inappropriate that individuals at some journals hide behind the journal name and avatar to use journal twitter accounts as a soapbox to express their personal opinions. This is a really dangerous thing for a journal to do since it reinforces stereotypes about the fickleness of editors that love to wield the power that their journal provides them. It’s also a bad idea since the opinions of one or a few people may unintentionally affect a journal or publisher.
• Do encourage your staff to create personal accounts and be active on social media. Editors and other journal staff should be encouraged to express personal opinions about science, tweet their own highlights, etc. This is a great way for Scientists to get to know your staff (for better or worse) and build an opinion about who is handling our work at your journal. But it should go without saying that personal opinions should be made through personal accounts, so we can follow/unfollow these people like any other member of the community and so their opinions do not leverage the imprimatur of your journal.
• Do use journal Twitter accounts to respond to feedback/complaints/queries. Directly replying to comments from the community on Twitter is a great way to build trust in your journal.  If you can’t or don’t want to reply to a query in the open, just reply by asking the person to email your helpdesk. Either way shows good faith that you are listening to our concerns and want to engage. Ignoring comments from Scientists is bad PR and can allow issues to amplify beyond your control, with possible negative impacts on your journal (image) in the long run.
• Don’t use journal Twitter accounts to tweet from meetings. To me this is a form of expressing personal opinion that looks like you are endorsing certain Scientists/fields/meetings or, worse yet, that you are looking to solicit them to submit their work to your journal, which smacks of desperation and favoritism. Use personal accounts instead to tweet from meetings, since after all what is reported is a personal assessment.

These are just my first thoughts on this issue (anonymised to protect the guilty), which I hope will act as a springboard for others to comment below on how they think journals should manage their presence on Twitter for the benefit of the Scientific community.

This PLOS Collection arose out of a twitter conversation with Theo Bloom last year, and has come together through the hard work of the authors of the papers in the Collection, the PLOS Collections team (in particular Sam Moore and Jennifer Horsely), and my co-organizers Larry Hunter and Andrey Rzhetsky. Many thanks to all for seeing this effort to completion.

Because of the large body of work in the area of text mining published in PLOS, we struggled with how best to present all these papers in the collection without diluting the experience for the reader. In the end, we decided only to highlight new work from the last two years and major reviews/tutorials at the time of launch. However, as this is a living collection, new articles will be included in the future, and the aim is to include previously published work as well. We hope to see many more papers in the area of text mining published in the PLOS family of journals in the future.

An overview of the PLOS Text Mining Collection is below (cross-posted at the PLOS EveryONE blog) and a commentary on Collection is available at the Official PLOS Blog entitled “A mine of information – the PLOS Text Mining Collection“.

Background to the PLOS Text Mining Collection

Text Mining is an interdisciplinary field combining techniques from linguistics, computer science and statistics to build tools that can efficiently retrieve and extract information from digital text. Over the last few decades, there has been increasing interest in text mining research because of the potential commercial and academic benefits this technology might enable. However, as with the promises of many new technologies, the benefits of text mining are still not clear to most academic researchers.

This situation is now poised to change for several reasons. First, the rate of growth of the scientific literature has now outstripped the ability of individuals to keep pace with new publications, even in a restricted field of study. Second, text-mining tools have steadily increased in accuracy and sophistication to the point where they are now suitable for widespread application. Finally, the rapid increase in availability of digital text in an Open Access format now permits text-mining tools to be applied more freely than ever before.

To acknowledge these changes and the growing body of work in the area of text mining research, today PLOS launches the Text Mining Collection, a compendium of major reviews and recent highlights published in the PLOS family of journals on the topic of text mining. As one of the major publishers of the Open Access scientific literature, it is perhaps no coincidence that research in text mining in PLOS journals is flourishing. As noted above, the widespread application and societal benefits of text mining is most easily achieved under an Open Access model of publishing, where the barriers to obtaining published articles are minimized and the ability to remix and redistribute data extracted from text is explicitly permitted. Furthermore, PLOS is one of the few publishers who is actively promoting text mining research by providing an open Application Programming Interface to mine their journal content.

Text Mining in PLOS

Since virtually the beginning of its history [1], PLOS has actively promoted the field of text mining by publishing reviews, opinions, tutorials and dozens of primary research articles in this area in PLOS Biology, PLOS Computational Biology and, increasingly, PLOS ONE. Because of the large number of text mining papers in PLOS journals, we are only able to highlight a subset of these works in the first instance of the PLOS Text Mining Collection. These include major reviews and tutorials published over the last decade [1][2][3][4][5][6], plus a selection of research papers from the last two years [7][8][9][10][11][12][13][14][15][16][17][18][19] and three new papers arising from the call for papers for this collection [20][21][22].
The research papers included in the collection at launch provide important overviews of the field and reflect many exciting contemporary areas of research in text mining, such as:

• methods to extract textual information from figures [7];
• methods to cluster [8] and navigate [15] the burgeoning biomedical literature;
• integration of text-mining tools into bioinformatics workflow systems [9];
• use of text-mined data in the construction of biological networks [10];
• application of text-mining tools to non-traditional textual sources such as electronic patient records [11] and social media [12];
• generating links between the biomedical literature and genomic databases [13];
• application of text-mining approaches in new areas such as the Environmental Sciences [14] and Humanities [16][17];
• named entity recognition [18];
• assisting the development of ontologies [19];
• extraction of biomolecular interactions and events [20][21]; and
• assisting database curation [22].

Looking Forward

As this is a living collection, it is worth discussing two issues we hope to see addressed in articles that are added to the PLOS text mining collection in the future: scaling up and opening up. While application of text mining tools to abstracts of all biomedical papers in the MEDLINE database is increasingly common, there have been remarkably few efforts that have applied text mining to the entirety of the full text articles in a given domain, even in the biomedical sciences [4][23]. Therefore, we hope to see more text mining applications scaled up to use the full text of all Open Access articles. Scaling up will maximize the utility of text-mining technologies and the uptake by end users, but also demonstrate that demand for access to full text articles exists by the text mining and wider academic communities.

Likewise, we hope to see more text-mining software systems made freely or openly available in the future. As an example of the state of affairs in the field, only 25% of the research articles highlighted in the PLOS text mining collection at launch provide source code or executable software of any kind [13][16][19][21]. The lack of availability of software or source code accompanying published research articles is, of course, not unique to the field of text mining. It is a general problem limiting progress and reproducibility in many fields of science, which authors, reviewers and editors have a duty to address. Making release of open source software the rule, rather than the exception, should further catalyze advances in text mining, as it has in other fields of computational research that have made extremely rapid progress in the last decades (such as genome bioinformatics).

By opening up the code base in text mining research, and deploying text-mining tools at scale on the rapidly growing corpus of full-text Open Access articles, we are confident this powerful technology will make good on its promise to catalyze scholarly endeavors in the digital age.

References

1. Dickman S (2003) Tough mining: the challenges of searching the scientific literature. PLoS biology 1: e48. doi:10.1371/journal.pbio.0000048.
2. Rebholz-Schuhmann D, Kirsch H, Couto F (2005) Facts from Text—Is Text Mining Ready to Deliver? PLoS Biol 3: e65. doi:10.1371/journal.pbio.0030065.
3. Cohen B, Hunter L (2008) Getting started in text mining. PLoS computational biology 4: e20. doi:10.1371/journal.pcbi.0040020.
4. Bourne PE, Fink JL, Gerstein M (2008) Open access: taking full advantage of the content. PLoS computational biology 4: e1000037+. doi:10.1371/journal.pcbi.1000037.
5. Rzhetsky A, Seringhaus M, Gerstein M (2009) Getting Started in Text Mining: Part Two. PLoS Comput Biol 5: e1000411. doi:10.1371/journal.pcbi.1000411.
6. Rodriguez-Esteban R (2009) Biomedical Text Mining and Its Applications. PLoS Comput Biol 5: e1000597. doi:10.1371/journal.pcbi.1000597.
7. Kim D, Yu H (2011) Figure text extraction in biomedical literature. PloS one 6: e15338. doi:10.1371/journal.pone.0015338.
8. Boyack K, Newman D, Duhon R, Klavans R, Patek M, et al. (2011) Clustering More than Two Million Biomedical Publications: Comparing the Accuracies of Nine Text-Based Similarity Approaches. PLoS ONE 6: e18029. doi:10.1371/journal.pone.0018029.
9. Kolluru B, Hawizy L, Murray-Rust P, Tsujii J, Ananiadou S (2011) Using workflows to explore and optimise named entity recognition for chemistry. PloS one 6: e20181. doi:10.1371/journal.pone.0020181.
10. Hayasaka S, Hugenschmidt C, Laurienti P (2011) A network of genes, genetic disorders, and brain areas. PloS one 6: e20907. doi:10.1371/journal.pone.0020907.
11. Roque F, Jensen P, Schmock H, Dalgaard M, Andreatta M, et al. (2011) Using electronic patient records to discover disease correlations and stratify patient cohorts. PLoS computational biology 7: e1002141. doi:10.1371/journal.pcbi.1002141.
12. Salathé M, Khandelwal S (2011) Assessing Vaccination Sentiments with Online Social Media: Implications for Infectious Disease Dynamics and Control. PLoS Comput Biol 7: e1002199. doi:10.1371/journal.pcbi.1002199.
13. Baran J, Gerner M, Haeussler M, Nenadic G, Bergman C (2011) pubmed2ensembl: a resource for mining the biological literature on genes. PloS one 6: e24716. doi:10.1371/journal.pone.0024716.
14. Fisher R, Knowlton N, Brainard R, Caley J (2011) Differences among major taxa in the extent of ecological knowledge across four major ecosystems. PloS one 6: e26556. doi:10.1371/journal.pone.0026556.
15. Hossain S, Gresock J, Edmonds Y, Helm R, Potts M, et al. (2012) Connecting the dots between PubMed abstracts. PloS one 7: e29509. doi:10.1371/journal.pone.0029509.
16. Ebrahimpour M, Putniņš TJ, Berryman MJ, Allison A, Ng BW-H, et al. (2013) Automated authorship attribution using advanced signal classification techniques. PLoS ONE 8: e54998. doi:10.1371/journal.pone.0054998.
17. Acerbi A, Lampos V, Garnett P, Bentley RA (2013) The Expression of Emotions in 20th Century Books. PLoS ONE 8: e59030. doi:10.1371/journal.pone.0059030.
18. Groza T, Hunter J, Zankl A (2013) Mining Skeletal Phenotype Descriptions from Scientific Literature. PLoS ONE 8: e55656. doi:10.1371/journal.pone.0055656.
19. Seltmann KC, Pénzes Z, Yoder MJ, Bertone MA, Deans AR (2013) Utilizing Descriptive Statements from the Biodiversity Heritage Library to Expand the Hymenoptera Anatomy Ontology. PLoS ONE 8: e55674. doi:10.1371/journal.pone.0055674.
20. Van Landeghem S, Bjorne J, Wei C-H, Hakala K, Pyysal S, et al. (2013) Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization. PLOS ONE 8: e55814. doi:10.1371/journal.pone.0055814
21. Liu H, Hunter L, Keselj V, Verspoor K (2013) Approximate Subgraph Matching-based Literature Mining for Biomedical Events and Relations. PLoS ONE 8(4): e60954. doi:10.1371/journal.pone.0060954
22. Davis A, Weigers T, Johnson R, Lay J, Lennon-Hopkins K, et al. (2013) Text mining effectively scores and ranks the literature for improving chemical-gene-disease curation at the Comparative Toxicogenomics Database. PLOS ONE 8: e58201. doi:10.1371/journal.pone.0058201
23. Bergman CM (2012) Why Are There So Few Efforts to Text Mine the Open Access Subset of PubMed Central? http://caseybergman.wordpress.com/2012/03/02/why-are-there-so-few-efforts-to-text-mine-the-open-access-subset-of-pubmed-central/.

Why are early stage researchers hit hardest by stagnation or decreases in funding? Simply because access to funding is not a level playing field for all scientists, and is in fact highly dependent on career stage and experience. Therefore, increased competition for resources is expected to hit younger scientists disproportionately harder relative to established researchers because of many factors, including:

• less experience in the art of writing grants,
• less experience in reviewing grants,
• less experience serving on grant panels,
• shorter scientific and management track record,
• and a less highly developed social network.

The specific negative effect that a general increase in resource competition has on young researchers is (in my view) the best explanation for the extremely worrying downward trends in the proportion of young PIs receiving NIH grants, and the increasing upward trend in the age to receipt of first RO1 in the USA, shown in the following diagrams from the NIH Rock Talk Blog:

Thankfully, this issue which is being discussed seriously by NIH’s Deputy Director for Extramural Research, Dr. Sally Rockey, as publication of these data attests to.  [I would very much welcome if other funding agencies published similar demographic breakdowns of their funding to address whether this is a global effect.] However, not all see these trends as worrying and interpret them on socially-neutral demographic grounds.

To help combat the inherent age-based iniquities in access research funding, funding agencies typically ring-fence funding for early-stage researchers under a “New Investigator” type umbrella. In fact, Sally Rockey provides a link to an impressive history of initiatives the NIH has undertaken to tackle the New Investigator issue. But what is striking to me is that despite putting a series of different New Investigator mechanisms in place, the negative impacts on early-stage researchers have only worsened over the last three decades. Thus New Investigator programmes are clearly not enough to redress this issue, and new solutions must be sought out. Furthermore ring-fencing funding for junior researchers necessarily creates an us-vs-them mentality, which can have counterproductive repercussions among different scientific cohorts. And while New Investigator programmes are widely supported in principle, trade-offs in resource allocation can lead to unstable to changes in policy, as witnessed in the case of the now-defunct NERC New Investigator programme.

So, what of it? Is this post just another bemoaning the sorry state of affairs in funding for early-stage researchers? No, or at least, not only. Actually, my motivation is to constructively propose a relatively simple (naive?) mechanism to fund research projects that can address the inequities in funding across career stages, but which also has the additional benefit of engendering mentorship and transfer of skills across the generations: the Junior/Senior Partnership Grant. [As with all (good) ideas, such a model has been proposed before by the Women's Cancer Network, but does not appear to be adopted by major federal funding agencies.]

The idea behind a Junior/Senior Partnership funding “scheme” is simple. Based on some criteria (years since PhD or first tenure-track position, number of successful PI awards, number of wrinkles, etc.) researchers would be classified as Junior or Senior. Based on your classification, to be eligible for an award under such a programme, at least one Junior and one Senior PI would need to be co-applicants on grant and have distinct contributions to the grant and project management. This simple mechanism would ensure that young PIs get a piece of the funding pie and allow them to establish a track record, just as a New Investigator schemes do.  But it would also obviate the need for reform to rely on the altruistic stepping aside by Senior scientists to make way for their Junior colleagues, as there would be positive (financial) incentives for them to lend a hand down the generations. And by reconfiguring resource allocation from “us-vs-them” to “we’re-all-in-this-together,” Junior/Senior Partnership Grants would further provide a natural mechanism for Senior PIs to transfer expertise in grant writing and project management to their Junior colleagues in a meaningful way, rather than in the lip-service manner that is normally paid in most institutions. Finally, and most importantly, the knowledge transfer through such a scheme would strengthen the future expertise base in Science, which all indicators would suggest is currently at risk.

Related Posts:

• Rock Talk: Our Commitment to Supporting the Next Generation.
• Rock Talk: Age Distribution of NIH Principal Investigators and Medical School Faculty.
• Geek Prof: Personal responsibility and research funding.
• Social Dimension: The Fate of Young Scientists.
• Simply Statistics: I’m a young scientist and sequestration will hurt me.

According to Brenner (1996) [1], the common use of the suffix “-on” in molecular biological terms can be traced to Seymour Benzer’s dissection of the fine structure of the rII locus in bacteriophage T4, which overturned the classical idea that a gene is an indivisible unit:

To mark this new view of the gene, Seymour invented new terms for the now different units of mutation, recombination and function. As he was a physicist, he modelled his terms on those of physics and just as electrons, protons and neutrons replaced the once indivisible atom, so genes came to be composed of mutons, recons and cistrons. The the unit of function, the cistron was based on the cis–trans complementation test, of which only the trans part is usually done…Of these terms, only cistron came to be widely used. It is conjectured that the other two, the muton and the recon, disappeared because Seymour failed to follow the first rule for inventing new words, which is to check what they may mean in other languages…Seymour’s pioneering invention of units was followed by a spate of other new names not all of which will survive. One that seems to have taken root is codon, which I invented in 1957; and the terms intron and exon, coined by Walter Gilbert, are certain to survive as well. Operon is moot; it is still frequently used in prokaryotic genetics but as the weight of research shifts to eukaryotes, which do not have such units of regulation, it may be lost. Replicon, invented by Francis Jacob and myself in 1962, seems also to have survived, despite the fact that we paid insufficient attention to how it sounded in other languages.

Thus, the fact that many molecular biological terms end in “-on” (initiated by Benzer) owes its origin to patterns of nomenclature in chemistry/nuclear physics (which itself began with Stoney’s proposal of the term electron in 1894) and the desire to identify “fundamental units” of biological structure and function.

While Brenner’s commentary provides a crucial first-hand account to understand the origin of these terms, it does not provide any primary references concerning the coining of these terms. So I’ve spent some time digging out the original usage for a number of more common molecular biology “-ons”, which I thought many be of use or interest to others.

The terms recon, muton and cistron were defined by Benzer (1957) [2] as follows:

• Recon: “The unit of recombination will be defined as the smallest element in the one-dimensional array that is interchangeable (but not divisible) by genetic recombination. One such element will be referred to as a “recon.”"

• Muton: “The unit of mutation, the “muton” will be defined as the smallest element that, when altered, can give rise to a mutant form of the organism.”

• Cistron: “A unit of function can be defined genetically, independent of biochemical information, by means of the elegant cis-trans comparison devised by [Ed] Lewis…Such a map segment, corresponding to a function which is unitary as defined by the cis-trans test applied to the heterocaryon, will be defined as a cistron.”

I have not been able to find a definitive first reference that defines the term codon the fundamental unit of the genetic code. According to Brenner (1996) [1] and US National Library of Medicine’s Profiles in Science webpage on Marshall Nirenberg [2], the term codon was introduced by Brenner in 1957 “to describe the fundamental units engaged in protein synthesis, even though the units had yet to be fully determined. Francis Crick popularized the term in 1959. After 1962, Nirenberg began to use “codon” to characterize the three-letter RNA code words” [3].

The term operon was introduced by Jacob et al. (1960) [4] and defined as follows (italics theirs):

• Operon: “Celle-ci comprendrait des unités d’expression coordonée (opérons) constituées par un opérateur et le group de gènes de structure coodoneés par lui.”

A couple of preliminaries. First, the main point of this post is not about trying to convince people to post preprints to arXiv. The benefits of preprinting on arXiv are manifold (early availability of results, allowing others to build on your work sooner, prepublication feedback on your manuscript, feedback from many eyes not just 2-3 reviewers, availability of manuscript in open access format, mechanism to establish scientific priority, opportunity to publicize your work in blogs/twitter, increased duration for citations) and have been ably summarized elsewhere. This post is specifically about how one can get the most out of preprinting on arXiv by using Google Scholar tools.

Secondly, it is important to make sure people are aware of two relatively recent developments in the Google Scholar toolkit beyond the basic Google Scholar search functionality — namely, Google Scholar Citations and Google Scholar Updates. Google Scholar Citations allows users to build a personal profile of their publications, which draws in citation data from the Google Scholar database, allowing you to “check who is citing your publications, graph citations over time, and compute several citation metrics”, which also will “appear in Google Scholar results when people search for your name.” While Google Scholar Citations has been around for a little over a year now, I often find that many Scientists are either not aware that it exists, or have not activated their profile yet, even though it is scarily easy to set up. Another more recent feature available for those with active Google Scholar Citations profiles is called Google Scholar Updates, a tool that can analyze “your articles (as identified in your Scholar profile), scan the entire web looking for new articles relevant to your research, and then show you the most relevant articles when you visit Scholar”. As others have commented, Google Scholar Updates provides a big step forward in sifting through the scientific literature, since it provides a tailored set of articles delivered to your browser based on your previous publication record.

With these preliminaries in mind, what I want to discuss now is how a Google Scholar plays so well with preprints on arXiv to accelerate science when done in the Open. By posting preprint to arXiv and activating your Google Scholar Citation profile, you immediately gain several advantages, including the following:

1. arXiv preprints are rapidly indexed by Google Scholar (with 1-2 days in my experience) and thus can be discovered easily by others using a standard Google Scholar search.
2. arXiv preprints are listed in your Google Scholar profile, so when people browse your profile for your most recent papers they will find arXiv preprints at the top of the list (e.g. see Graham Coop’s Google Scholar profile here).
3. Citations to your arXiv preprints are automatically updated in your Google Scholar profile, allowing you to see who is citing your most recent work.
4. References included in your arXiv preprints will be indexed by Google Scholar and linked to citations in other people’s Google Scholar profiles, allowing them to find your arXiv preprint via citations to their work.
5. Inclusion of an arXiv preprint in your Google Scholar profile allows Google Scholar Updates to provide better recommendations for what you should read, which is particularly important when you are moving into a new area of research that you have not previously published on.
6. [Update June 14, 2013] Once Google Scholar has indexed your preprint on arXiv it will automatically generate a set of Related Articles, which you can browse to identify previously published work related to your manuscript.  This is especially useful at the preprint stage, since you can incorporate related articles you may have missed before submission or during revision.
   

I probably have overlooked other possible benefits of the synergy between these two technologies, since they are only dawning on me as I become more familiar with these symbiotic scholarly tools myself. What’s abundantly clear to me at this stage though is that by embracing Open Science and using arXiv together with Google Scholar puts you at a fairly substantial competitive advantage in terms of your scholarship, in ways that are simply not possible using the classical approach to publishing in biology.

To see how this ethical issue arises, I’ll first describe my current workflow for submitting to arXiv and publicizing it on Twitter. Then, I’ll propose an alternative that might be considered to be “gaming” the system, and discuss precedents in the pre-social media world that might inform the resolution of this issue.

My current workflow for submission to arXiv and announcement on twitter is as follows:

1. submit manuscript to a journal with suggested reviewers based on personal judgement;
2. deposit the same version of the manuscript that was submitted to journal in arXiv;
3. wait until arXiv submission is live and then tweet links to the arXiv preprint.

From doing this a few times (as well as benefiting from additional Twitter exposure via Haldane’s Sieve), I’ve realized that there can often be fairly substantive feedback about an arXiv submission via twitter in the form of who (re)tweets links to it and what people are saying about the manuscript. It doesn’t take much thought to realize that this information could potentially be used to influence a journal submission in the form of which reviewers to suggest or oppose using an alternative workflow:

1. submit manuscript to arXiv;
2. wait until arXiv submission is live and then tweet about it;
3. moniter and assimilate feedback from Twitter;
4. submit manuscript to journal with suggested and opposed reviewers based on Twitter activity.

This second workflow incidentally also arises under the first workflow if your initial journal submission is rejected, since there would naturally be a time lag in which it would be difficult to fully ignore activity on Twitter about an arXiv submission.

Now, I want to be clear that I haven’t and don’t intend to use the second workflow (yet), since I have not fully decided if this an ethical approach to suggesting reviewers. Nevertheless, I lean towards the view that it is no more or less ethical than the current mechanisms of selecting suggested reviewers based on: (1) perceived allies/rivals with relevant expertise or (2) informal feedback on the work in question presented at meetings.

In the former case of using who you perceive to be for or against your work, you are relying on personal experience and subjective opinions about researchers in your field, both good and bad, to inform your choice of suggested or opposed reviewers. This is some sense no different qualitatively to using information on Twitter prior to journal submission, but is instead based on a closed network using past information, rather than an open network using information specific to the piece of work in question. The latter case of suggesting reviewers based on feedback from meeting presentations is perhaps more similar to the matter at hand, and I suspect would be considered by most scientists to be a perfectly valid mechanism to suggest or oppose reviewers for a journal submission.

Now, of course I recognize that suggested reviewers are just that, and editors can use or ignore these suggestions as they wish, so this issue may in fact be moot. However, based on my experience, suggested reviewers are indeed frequently used by editors (if not, why would they be there?). Thus resolving whether smoking out opinions on Twitter is considered “fair play” is probably something the scientific community should consider more thoroughly in the near future, and I’d be happy to hear what other folks think about this in the comments below.

Just to see how easy this is, I’ve copied the process for deleting a repository on github here:

• Go to the repo’s admin page

• Click “Delete this repository”

• Read the warnings and enter the name of the repository you want to delete

• Click “I understand the consequences, delete this repository

Given the increasing use of github in publications, I feel the issue of repository deletion on github needs to be discussed by scientists and publishers more in the context of the important issue of long-term maintenance of published code. The reason I see this as important is that most github repositories are published via individual user accounts, and thus only one person holds the keys to preservation of the published code. Furthermore, I suspect funders, editors, publishers and (most) PIs have no idea how easy it is under the current model to delete published code. Call me a bit paranoid, but I see it is my responsibility as a PI to ensure the long-term preservation of published code, since I’m the one who signs off of data/resource plans in grants/final reports. Better to be safe than sorry, right?

On this note, I was pleased to see a retweet in my stream this week (via C. Titus Brown) concerning news that the journal Computers & Geosciences has adopted an official policy for hosting published code on github:

Computers & Geosciences journal formally adopts github for all new code they publish! iamg.org/index.php/publ…—
Fernando Perez (@fperez_org) November 02, 2012

The mechanism that Computers & Geosciences has adopted to ensure long-term preservation of code in their journal is very simple – for the editor to fork code submitted by a github user into a journal organization (note: a similar idea was also suggested independently by Andrew Perry in the comments to my previous post). As clearly stated in the github repository deletion mechanism “Deleting a private repo will delete all forks of the repo. Deleting a public repo will not.” Thus, once Computers & Geosciences has forked the code, risk to the author, journal and community of a single point of failure is substantially ameliorated, with very little overhead to authors or publishers.

So what about the many other journals that have no such digital preservation policy but currently publish papers with bioinformatics code in github? Well, as a stopgap measure until other journals get on board with similar policies (PLOS & BMC, please lead the way!), I’ve taken the initiative to create a github organization called BioinformaticsArchive to serve this function. Currently, I’ve forked code for all but one of the 64 publications with github URLs in their PubMed record. One of the scary/interesting things to observe from this endeavor is just how fragile the current situation is. Of the 63 repositories I’ve forked, about 50% (n=31) had not been previously forked by any other user on github and could have been easily deleted, with consequent loss to the scientific community.

I am aware (thanks to Marc Robinson Rechavi) there are many more published github repositories in the full-text of articles (including two from our lab), which I will endeavor to dig out and add to this archive asap. If anyone else would like to help out with the endeavor, or knows of published repositories that should included, send me an email or tweet and I’ll add them to the archive. Comments on how to improve on the current state of preservation of published bioinformatics code on github and what can be learned form Computers and Geosciences new model policy are most welcome!

Over the last two weeks, a meme has been making the rounds in the scientific twittersphere that goes something like “Rejection of a scientific manuscript improves its eventual impact”.  This idea is based a recent analysis of patterns of manuscript submission reported in Science by Calcagno et al., which has been actively touted in the scientific press and seems to have touched a nerve with many scientists.

Nature News reported on this article on the first day of its publication (11 Oct 2012), with the statement that “papers published after having first been rejected elsewhere receive significantly more citations on average than ones accepted on first submission” (emphasis mine). The Scientist led its piece on the same day entitled “The Benefits of Rejection” with the claim that “Chances are, if a researcher resubmits her work to another journal, it will be cited more often”. Science Insider led the next day with the claim that “Rejection before publication is rare, and for those who are forced to revise and resubmit, the process will boost your citation record”. Influential science media figure Ed Yong tweeted “What doesn’t kill you makes you stronger – papers get more citations if they were initially rejected”. The message from the scientific media is clear: submitting your papers to selective journals and having them rejected is ultimately worth it, since you’ll get more citations when they are published somewhere lower down the scientific publishing food chain.

I will take on faith that the primary result of Calcagno et al. that underlies this meme is sound, since it has been vetted by the highest standard of editorial and peer review at Science magazine. However, I do note that it not possible to independently verify this result since the raw data for this analysis was not made available at the time of publication (contravening Science’s “Making Data Maximally Available Policy“), and has not been made available even after being queried. What I want to explore here is why this meme is so uncritically being propagated in the scientific press and twittersphere.

As succinctly noted by Joe Pickrell, anyone who takes even a cursory look at the basis for this claim would see that it is at best a weak effect*, and is clearly being overblown by the media and scientists alike.

For everyone excited about the evidence that rejected papers are more cited, here's the relevant figure. Still excited? http://t.co/C3VHJWi3—
Joe Pickrell (@joe_pickrell) October 12, 2012

Taken at face value, the way I read this graph is that papers that are rejected then published elsewhere have a median value of ~0.95 citations, whereas papers that are accepted at the first journal they are submitted to have a median value of ~0.90 citations. Although not explicitly stated in the figure legend or in the main text, I assume these results are on a natural log scale since, based on the font and layout, this plot was most likely made in R and the natural scale is the default in R (also, the authors refer the natural scale in a different figure earlier in the text). Thus, the median number of citations per article that rejection may provide an author is on the order of ~0.1.  Even if this result is on the log10 scale, this difference translates to a boost of less than one citation.  While statistically significant, this can hardly be described as a “significant increase” in citation. Still excited?

More importantly, the analysis of the effects of rejection on citation is univariate and ignores all most other possible confounding explanatory variables.  It is easy to imagine a large number of other confounding effects that could lead to this weak difference (number of reviews obtained, choice of original and final journals, number of authors, rejection rate/citation differences among discipline or subdiscipline, etc., etc.). In fact, in panel B of the same figure 4, the authors show a stronger effect of changing discipline on the number of citations in resubmitted manuscripts. Why a deeper multivariate analysis was not performed to back up the headline claim that “rejection improves impact” is hard to understand from a critical perspective. [UPDATE 26/10/2012: Bala Iyengar pointed out to me a page on the author's website that discusses the effects of controlling for year and publishing journal on the citation effect, which led me to re-read the paper and supplemental materials more closely and see that these two factors are in fact controlled for in the main analysis of the paper. No other possible confounding factors are controlled for however.]

So what is going on here? Why did Science allow such a weak effect with a relatively superficial analysis to be published in the one of the supposedly most selective journals? Why are major science media outlets pushing this incredibly small boost in citations that is (possibly) associated with rejection? Likewise, why are scientists so uncritically posting links to the Nature and Scientist news pieces and repeating “Rejection Improves Impact” meme?

I believe the answer to the first two questions is clear: Nature and Science have a vested interest in making the case that it is in the best interest of scientists to submit their most important work to (their) highly selective journals and risk having it be rejected.  This gives Nature and Science first crack at selecting the best science and serves to maintain their hegemony in the scientific publishing marketplace. If this interpretation is true, it is an incredibly self-serving stance for Nature and Science to take, and one that may back-fire since, on the whole, scientists are not stupid people who blindly accept nonsense. More importantly though, using the pages of Science and Nature as a marketing campaign to convince scientists to submit their work to these journals risks their credibility as arbiters of “truth”. If Science and Nature go so far as to publish and hype weak, self-serving scientometric effects to get us to submit our work there, what’s to say that would they not do the same for actual scientific results?

But why are scientists taking the bait on this one?  This is more difficult to understand, but most likely has to do with the possibility that most people repeating this meme have not read the paper. Topsy records over 700 and 150 tweets to the Nature News and Scientist news pieces, but only ~10 posts to the original article in Science. Taken at face value, roughly 80-fold more scientists are reading the news about this article than reading the article itself. To be fair, this is due in part to the fact that the article is not open access and is behind a paywall, whereas the news pieces are freely available**. But this is only the proximal cause. The ultimate cause is likely that many scientists are happy to receive (uncritically, it seems) any justification, however tenuous, for continuing to play the high-impact factor journal sweepstakes. Now we have a scientifically valid reason to take the risk of being rejected by top-tier journals, even if it doesn’t pay off. Right? Right?

The real shame in the “Rejection Improves Impact” spin is that an important take-home message of Calcagno et al. is that the vast majority of papers (>75%) are published in the first journal to which they are submitted.  As a scientific community we should continue to maintain and improve this trend, selecting the appropriate home for our work on initial submission. Justifying pipe-dreams that waste precious time based on self-serving spin that benefits the closed-access publishing industry should be firmly: Rejected.

Don’t worry, it’s probably in the best interest of Science and Nature that you believe this meme.

* To be fair, Science Insider does acknowledge that the effect is weak: “previously rejected papers had a slight bump in the number of times they were cited by other papers” (emphasis mine).

** Following a link available on the author’s website, you can access this article for free here.

References
Calcagno, V., Demoinet, E., Gollner, K., Guidi, L., Ruths, D., & de Mazancourt, C. (2012). Flows of Research Manuscripts Among Scientific Journals Reveal Hidden Submission Patterns Science DOI: 10.1126/science.1227833

Related Posts

• Cheap Talk – Rejection Improves Your Papers?
• Vincent Calcagno research – The benefits of rejection, continued
• LSE Impact of Social Sciences – The hidden map of science: Pre-publication history of articles tells us that rejection leads to higher citations