European Plant Biotech in the Balance

These are pivotal times for plant biotechnology in Europe. The new European Commissioner for Health and Food Safety, Vyentis Andriukaitis, is not due to take up his role until the 1st November but he already knows that the current rules on genetically modimied crops create conflicts between the commission itself and the member states. Those rules have seen only two GM crops licensed to be grown commercially in the EU in almost 15 years: Monsanto’s insect resistant MON810 maize and  BASF’s Amflora potato, of which the later was withdrawn from commercialisation in 2012.

BürGenLand_(2010)

Protests against the cultivation of the genetically modified potato variety Amflora contributed to its withdrawal from commercial use in 2012.
{credit}”BürGenLand (2010)” by BASFPlantScience – Licensed under Creative Commons Attribution 2.0 via Wikimedia Commons{/credit}

Four days after Mr Andriukatis takes office the European Parliament’s environment, public health and food safety (ENVI) committee scheduled to give its opinion on a draft report that could change the regulations concerning the ‘release’ of GMOs and thus their use as crops. Many believe that rather than relaxing the regulations the European Parliament may extend its de-facto ban on GM plants leaving european plant biotechnology efforts ‘dead and buried‘. Not that it is entirely clear what is meant by ‘genetically modified’ in this day and age when techniques for genome editing can alter a plants genetic makeup in highly precise ways but leave no transgenic material behind (see Sense About Sciences excellent online discussion of this topic held earlier this week). Such developments have been used by the UK’s Biotechnology and Biological Sciences Research Council (BBSRC) to push for a wholly new regulatory framework for GM crops.

Against this background twenty one leading plant scientists working in Europe have published an open letter calling on the Decision Makers of Europe to back research into plant biotechnology through funding, legislation and support. They point out that  Twenty-one people may not seem like many these are drawn from the thirty most cited authors in plant science in Europe. The letter has been co-odinated by Stefan Jansson of Umeå University, Sweden, who points out that this is not “a list of scientists with links to industry who some might say ‘would say that anyway’. Rather he has assembled European plants sciences’ the most influential academic researchers; saying “politicians that choose to ignore this message cannot in the future say that they take science seriously.”

Will such calls fall on deaf ears or reap future rewards? Judge for yourself as here is the text of the letter in full:

 

Open letter to decision makers in Europe

We all depend on plants for providing us with food, building material, textiles, medicine and fuel. Among the greatest challenges facing mankind are the provision of healthy and nutritious food, feed and fuel to a burgeoning population using agricultural and forestry practices that are environmentally and economically sustainable. Thanks to basic research on plants, we now understand well how plants grow, how they protect themselves against disease and environmental stress, and what factors limit production in agriculture and forestry.

Europe has a strong history of plant science. Robert Hooke introduced the concept of the “cell” in the 17th century after looking at cork slivers in his microscope. Carl Linnaeus developed systematics after his studies of plants and Gregor Mendel deciphered the laws of genetics after meticulous counting of plants in his monastery garden in Brno. Plant scientists discovered chromosomes, enzymes and viruses, and Charles Darwin spent a large part of his scientific career as a plant biologist; “The origin of species” starts “When we look to the individuals of the same variety or sub- variety of our older cultivated plants and animals…”. Curiosity-driven plant research has been important both to deepen our understanding of nature and take benefit of it, still we lack basic understanding of many complex phenomena in plants.

27 of the “30 most cited authors in plant science” in Europe (https://www.labtimes.org/labtimes/ranking/2013_04/index2.lasso) hold at present a position at a publicly funded research organization in Europe, and 21 out of the 27 have signed this letter. We work on various aspects of plant science, for example systematics, physiology, biochemistry, molecular biology, genetics, ecophysiology, ecology, pathology, biodiversity and effects of climate change. It is possible to perform good curiosity-driven plant science in Europe and we acknowledge our support from various funding bodies, in many respects plant science in Europe is doing well.

However, well is not good enough. Plant science has arguably contributed more to the reduction of human suffering than biomedical research, yet compared with the latter it is hugely underfunded worldwide. Norman Borlaug’s dwarf and rust-resistant varieties of wheat saved many millions from hunger. Basic science performed in Europe is also an efficient way of supporting applied research in poorer countries. We are concerned that Europe will have serious problems in reaching its ambitions of Horizon 2020: to “tackle societal challenges” and “to ensure Europe produces world- class science, removes barriers to innovation and makes it easier for the public and private sectors to work together in delivering innovation” and see three outstanding issues for decision makers to address.

First, to provide solutions to the societal challenges outlined in Horizon 2020 funding for fundamental and applied plant science should be maintained or, if possible, be increased. Most importantly, serious challenges are not adequately addressed, such as developing plants resilient to climate change, preventing loss of crop biodiversity, and creating an agriculture that avoids unsustainable demands for water, energy, fertilizers and pesticides. These tasks must be addressed in forthcoming Horizon 2020 calls.

Secondly, plant scientists must be able to perform field experiments. Many of us work with genetically modified plants as research tools, for example to understand how native plants and crops protect themselves against pests and will react to climate change. However, in most European countries permits to perform field experiments with transgenic plants are blocked, not on scientific but on political grounds. In countries that do permit field experiments, these are often systematically vandalized, causing huge scientific and financial losses. Some of us have even been threatened and had private property vandalized. This is a serious threat to science, to publicly funded research, and to European society itself. European authorities must ensure that approved and safe field experiments with transgenic plants are made possible. Vandals must be prosecuted and held accountable for scientific and financial damage.

Thirdly, Europe must allow prompt authorization of genetically modified plant varieties that have been found safe by the competent authority following a thorough science-based risk evaluation. This is essential to meet the Horizon 2020 goal of removing barriers to innovation and making it easier for the public and private sectors to work together in delivering innovation. The de facto moratorium on transgenic plant approvals has been detrimental for applied plant science and has effectively eliminated possibilities for publicly funded scientists and small companies to address the big challenges for society. The resulting reduced competition has enhanced the dominance of the major seed and agrochemical corporations. We believe that a fundamental revision of GM regulation is needed that strictly follows principles of a science-based evaluations and approvals, based on evaluation of the trait, rather than the method by which it is achieved.

Our scientific credibility comes from our work on basic plant science. Some of us also apply our knowledge to improving plants for the human society, but the reason that we make this statement is not commercial interests or hope of attracting more funding for our own research. Instead, we are seriously concerned that lack of adequate funding and safe infrastructures will relegate European basic and applied plant science to a second tier status. If plant scientists cannot apply their knowledge for the benefit of society, Europe will be unable to lead in global efforts to build a sustainable agricultural system and plant-based bio-economy. The most pressing global problems – how do deal with environmental change and secure food supply for all – arguably will only be solved with a massively increased worldwide investment in plant research.

Ian T. Baldwin, Director, Max Planck Institute for Chemical Ecology, Jena, Germany
Member of the US National Academy of Sciences
Member of the German National Academy of Sciences Leopoldina Member of the Berlin Brandenburgische Academy of Sciences

David C. Baulcombe, Regius Professor of Botany and Royal Society Research Professor, Plant Sciences, University of Cambridge, United Kingdom
Member of Academia Europaea
Foreign Associate Member of the US National Academy of Sciences
Foreign Associate Member of the National Academy of Sciences India Fellow of the Royal Society
Member of EMBO
Recipient of Wolf Prize for Agriculture
Recipient of Balzan Prize (Epigenetics)
Recipient of Lasker Prize for Basic Biomedical Science Recipient of Gruber Prize for Genetics

Nina Buchmann, Professor of Grassland Sciences, Institute of Agricultural Sciences, Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland
Founding member of the Young Academy of Sciences
Former member of the German Advisory Council for the Government on Global Change (WBGU)
Member of the German National Academy of Sciences Leopoldina Member of the Board of Trustees of the Öko-Institut e.V
Chair of the World Food System Center (WFSC) at ETH

Mark W. Chase, Keeper of the Jodrell Lab, Royal Botanic Gardens, Kew, Richmond, United Kingdom
Fellow of the Royal Society
Recipient of Veitch Memorial Medal by the Royal Horticultural Society (UK

Alisdair R. Fernie, Research group leader, Max Planck Institute for Molecular Plant Physiology, Potsdam, Germany.
Recipient of the Society of Experimental Biology medal (Plants)
Recipient of the Phytochemical Society of Europe Prize

Christine H. Foyer, Professor of Plant Sciences and Director of Africa College, University of Leeds, Leeds, UK
Winthrop Professor, The University of Western Australia, Australia
Pao Yu-Kong Chair Professor, Zhejiang University, China;
Recipient of Redox Pioneer award
Recipient if the Founders Award (American Society of Plant Physiologists).

Jiri Friml, Professor, Institute of Science and Technology (IST), Austria, Klosterneuburg, Austria
Member of EMBO
Fellow of the American Association for the Advancement of Science Recipient of Otto Hahn Medal
Recipient of VolkswagenStiftung Award
Recipient of Heinz Maier-Leibnitz Prize Recipient of Odysseus Award
Recipient of Olchemim Scientific Award Recipient of Körber European Science Award Recipient of EMBO Gold Medal

Jonathan Gershenzon, Director, Max Planck Institute for Chemical Ecology, Jena, Germany
Member, American Association for the Advancement of Sciences

Wilhelm Gruissem, Professor, Department of Biology, Plant Biotechnology, Eidgenössische Technische Hochschule (ETH) Zürich, , Switzerland
Fellow, American Association for the Advancement of Sciences
Fellow and Corresponding Member, American Society of Plant Biologists Recipient of the Anniversary Prize of the Fiat Panis Foundation
Recipient of the Shang Fa Yang Award of Academia Sinica Former President of the European Plant Science Organization Chair of the Global Plant Council

Dirk Inzé, Director, Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Ghent University, Belgium
Member of Royal Flemish Academy of Belgium for Science and the Arts Member of EMBO
Recipient of the Körber Stiftung Prize
Recipient of the Francqui Prize
Recipient of the Five-yearly FWO-Excellence Prize:
Recipient of the Dr A. De Leeuw-Damry-Bourlart in Exact Sciences Prize Chairperson of the Life Sciences, Environmental Sciences and Geosciences (LEGS) Committee of Science Europe

Stefan Jansson, Professor in Plant Cell and Molecular Biology, Umeå Plant Science Centre (UPSC), Plant Physiology, Umeå University, Sweden.
Member of the Royal Swedish Academy of Sciences
Recipient of Roséns Linneus Prize

Jonathan D. G. Jones, Professor, The Sainsbury Laboratory, Norwich, United Kingdom
Fellow of the Royal Society
Member of EMBO

Joachim Kopka, Research group leader. Max Planck Institute for Molecular Plant Physiology, Potsdam, Germany

Thomas Moritz, Professor, Umeå Plant Science Centre (UPSC) Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Sweden
Director Swedish Metabolomics Centre

Corné M. J. Pieterse, Director, Institute of Environmental Biology, Utrecht University
Member of the Royal Netherlands Academy of Arts and Sciences

Stephane Rombauts, Principal scientific staff, Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Ghent University, Belgium

Ben Scheres, Professor in Plant Developmental Biology, Wagenignen University, Netherlands
Member of the Dutch Royal Acadamy of Arts and Sciences
Recipient of Siron Pelton Award USA
Recipient of SPINOZA award

Bernhard Schmid, Professor of Environmental Sciences, Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Switzerland
Dean of the Faculty of Science

Mark Stitt, Prof Dr. Dr, h.c. Director, Max Planck Institute for Molecular Plant Physiology, Potsdam, Germany
Member of the German National Academy of Sciences Leopoldina
Honarary Doctor of Umeå University
Recipient of the Presidents medal, Society of Experimental Biology

Yves Van de Peer, Professor in Bioinformatics and Genome Biology, Ghent University, Belgium
Group leader, Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Belgium
Adjunct Professor, University of Western Ontario, Canada
Part-time Professor, Genomics research institute, University of Pretoria, South Africa Member of Royal Flemish Academy of Belgium for Science and the Arts

Detlef Weigel, Director, Max Planck Institute for Developmental Biology, Tübingen, Germany
Foreign Member of the Royal Society
Member of the US National Academy of Sciences
Member of the German National Academy of Sciences Leopoldina
Fellow of the American Association for the Advancement of Science Corresponding Member of the Heidelberg Academy of Sciences and Humanities Recipient of State Research Prize of Baden-Württemberg
Recipient of Otto Bayer Award
Recipient of Gottfried Wilhelm Leibniz Award

New Shoots at the NAS

I know that this is pretty much old news as the announcement of the new members of the National Academy of Sciences was made almost a month ago. However I’d very much like to congratulate all 84 new members and the 21 new foreign associates. But this is a blog dedicated to things planty so I’d lie to give special congratulations to those of the 105 who are plant researchers:

nas_logo

  • Edward Buckler; USDA Agricultural Research Service; and adjunct professor, department of plant breeding and genetics, College of Agriculture and Life Sciences, Cornell University, Ithaca, N.Y.
  • Kenneth Keegstra; University Distinguished Professor, department of biochemistry and molecular biology and department of plant biology, Michigan State University, East Lansing
  • John Pickett; Michael Elliott Distinguished Research Fellow and scientific leader of chemical ecology, Rothamsted Research, Harpenden, United Kingdom
  • Scott Poethig; Patricia M. Williams Professor of Biology, department of biology, University of Pennsylvania, Philadelphia

 

All four great scientists and very nice people as well.

Convivial Rice, Decoded Cotton and Bronze Medals

Last week was a busy week for Nature Plants for a number of reasons. Various members of the team were out at meetings so if you were at the TIP conference on the “Dynamics of Plant DNA” in Strasbourg you might have run into Guillaume. While if you were at UK Plant Sciences meeting on “Breeding plants for the future” you could have had the opportunity to chat with Anna over coffee.

What with all that, plus getting to grips with the first official submissions to the journal there wasn’t much time for blogging. There is nothing staler than old news so while they are still semi fresh in my mind here are some of the interesting things that I saw last week and intended to write about, but didn’t quite get to:

  • Timely focus on Photosynthesis
    The BBC radio 4 program “In our Time” tackled the question of photosynthesis this week with a discussion between Sandy Knapp, Nick Lane and John Allan. Great fun and well worth listening again to.
  • Table Manners
    Science published a provocative article called “Large-Scale Psychological Differences Within China Explained by Rice Versus Wheat Agriculture” which looked at different areas of China that either primarily dependent on rice or wheat culture. It seems that growing rice results in a more “interdependent and holistic-thinking” population. If you haven’t time to reads the article itself there is a good summary in the accompanying perspective, “Rice, Psychology, and Innovation“.
  • Barn-raised Biotech
    There was a nice piece on the TechRepublic blog about ‘Open Source Agriculture’. It talks about the Open Source Seed initiative that, taking its cue from Open Source software, is developing ways to distribute seeds in a way that makes them “available in perpetuity in a protected commons”.
  • Roses are red, Tomatoes are blue
    Cathie Martin and Eugenio Butelli of the John Innes Centre won the BBSRC Innovator of the Year award for their development of food varieties with enhanced vitamin contents, most notable their high-anthocyanin tomatoes.
  • Cotton Genomics
    Nature Genetics has published the genome sequence of tree cotton, Gossypium arboreum, from a team of researchers, principally based at the Institute of Cotton Research of the Chinese Academy of Agricultural Sciences. This is not only one of the major cultivated diploid species of cotton but also provides the major part of the genetic material of tetraploid cotton.
  • Prize Design
    The maize Genetics Executive committee has already announced that the first recipient of he Barbara McClintock Prize for Plant Genetics and Genome Studies will be David Baulcombe. What they don’t know yet is what that prize will look like. So they have started a further competition to design the prize, “a bronze medal (60 millimeters in diameter, 4 millimeters in thickness) that will carry a picture of Dr McClintock on one side and an image symbolizing one or more of her unique scientific contributions on the other”.

Protocols Discussion Forum is Moving

As you may or may not know Nature Protocols has a Discussion Forum where anyone having problems with their experiments can ask questions and hopefully receive helpful advice from other researchers with some experience in whatever is causing the problems. For the last several years this has been hosted on Nature Network but as of, well right about now, we are shifting its platform to a Google Group.

We have always thought of Nature Protocols as more than a journal and we try to engage with our readers to help them in their research. We have done this through commenting on our manuscripts; this blog; our YouTube channel and the discussion forum. We are always on the look out for technologies that might be helpful.

That’s why we are now moving the Discussion Forum onto the Google Groups platform.  We hope that this will greatly improve the effectiveness of the discussions by making it even easier for anyone to become involved in the forum. It should be easier to access on mobile devices, and easier to post on as comments can be made and discussion topics started simply by sending an email to nature-protocols-discussion@googlegroups.com.There are other technical advantages for us as well, not least a better spam filtering system so hopefully far fewer topics or posts will be offering fake passports for sale!

There are two ways to access the new look discussion forum, either through the Discussion page on this blog or directly at Google Groups . We very much hope that this move will increase the usefulness of the Discussion Forum by making it easier for researchers to take part, easier for the topics to be found by people searching for answers using search engines, and easier for topics to be connected to from throughout the Web.

The Current Discussion Forum isn’t going away but will remain as an archive. However it will not be possible to post new topics or reply to existing threads. I have however copied across all discussions started this year into the new platform as well as some of the most active from 2012. If there are any threads that you would like to see continued please let me know and I will copy those across as well.

I hope that everyone will find the new forum at least as helpful as it’s predecessor.

So, what shall we talk about? As an eponymous fictional talk show psychiatrist didn’t quite say:

“We’re listening.”

 

Deadline Roulette

I didn’t mean to write about peer review again. Two things I never mean to write about are Peer Review and Impact Factors, but being an editor provides a privileged viewpoint on both so I seem to keep coming back to them. And here we go again:

This time the spur is a new paper in Scientific Reports that caught my eye called “How Important Tasks are Performed: Peer Review“. I wrote last month about the psychology of setting deadlines for referees

and so this line in the abstract made me sit up and take notice:  “the time a referee takes to write a report on a scientific manuscript depends on the final verdict”. The phrase “a Deadline-effect” also appears in the abstract. My interest was piqued. Did the authors have real data? Were they going to conclude that setting different length deadlines could change the decision on a manuscript?

Fractions of various decision: classes accepted (I), accepted with minor revision (II), to be revised (III), rejected (IV), not appropriate (V) from all reports (as an inset the same for short-duration processes) . Adapted from Figure 2b of ref. 1

Fractions of various decision: classes accepted (I), accepted with minor revision (II), to be revised (III), rejected (IV), not appropriate (V) from all reports (as an inset the same for short-duration processes) . Adapted from Figure 2b of ref. 1

The authors have looked at data from two journals: Journal of High Energy Physics (JHEP) and the Journal of Statistical Mechanics: Theory and Experiment (JSTAT). The journals don’t really matter, what is important is that they have access to data from these journals of every interaction with referees giving times for responses to review requests, how long it took them to return reports and what the decision was (on the paper). From this they can do lots of plotting of decision times and see that things seem to be covered by Poisson statistics which means that they can do some mathematical modelling. They also see that for those reports that come back fast, that is within a day, there is a much higher proportion of clear cut decision: Accept as is, or Reject.

I don’t think that either of those observations will surprise many people but there is more. For a start the two journals have different reviewing deadlines. JSTAT asks for reviews in 3 weeks, JHEP in 4. Both slower than Nature Protocols but then this is physics, a foreign country where they do things differently. Their data don’t support my comments on deadlines though because the shape of the distribution of return times for reviews is the same for both journals just that JHEP’s is spread over a longer scale.

Now because the distributions they get are Poisson looking they can be modelled with a series of stochastic steps. Referees are seen as people who spend their days doing little bits of action (sub tasks) each one taking about 10 minutes, that add up to a whole task. Every 10 minutes (approximately) the referee chooses what subtask to do based on importance of the overall tasks.  If that were all though the distributions wouldn’t be as they are, there would be power-laws involved and a long tail of reports that take a very long time to be completed. What stops this happening is the ‘Deadline-effect’. Because there is a deadline set on the task the referees know they have to spend a set amount of time before the deadline on the report. The clear-cut reports come in more quickly not because they have fewer sub-tasks but rather because the referees assess from the outset that these are going to be ‘easier’ sub-tasks to complete and so are likely to perform them with higher probability. Always pick the low hanging fruit first!

I can’t quite decide what take home message I have from this paper. It certainly suggests that clear deadlines and ruthless chasing are needed to get reports from referees. Perhaps though there is also a lesson for authors: If you want to get your paper reviewed swiftly, make it as easy as possible to review. That it took almost 3 months for this paper to pass through review might suggest that is a conclusion the authors didn’t draw for themselves.

1. Hartonen, T. & Alava, M. J. How important tasks are performed: peer review. Scientific Reports 3, 1679 doi:10.1038/srep01679

Model Behaviour

Model organisms are much used in modern biology. Generally small and easy to keep in the lab, these creatures serve as the ‘typical example’ of a type of organism or biological process. Fruitflies, mice, yeast, zebra fish, Arabidopsis, etc. The list of organisms that can be regarded as models sometimes seems so long that the concept is itself undermined; how long before we see the platypus championed as a model? Nevertheless the use of ‘standard’ creatures does allow the results from different laboratories across the world to be directly compared, always assuming that these labs are treating their models in a standard way.

nematostellacoverFor the study of critical steps in animal development researchers are increasingly turning to the cnidarians, a phylum that includes jellyfish and corals, as they retain relatively simple body plans and yet are more clearly multi-cellular organisms than the somewhat colonial sponges. This week we have published four protocols concerning the cnidarian Nematostella vectensis, more commonly known as the starlet sea anemone, to act as a very basic ‘starter kit’ for anyone wishing to work with this organism.

Nematostella is a native of the east coast of the United States. It spends its time buried in mud feeding through its mouth, which is surrounded by two rings of tentacles. Slightly paradoxically they are classed as ‘vulnerable’ by the International Union for Conservation of Nature, but are also behaving as invasive aliens on the south coast of England and the west coast of the United States. But they grow fast and prolifically in the lab and have a sequenced genome1.nprot_2013_044-F5

The four protocols take us through some essential steps in working with Nematostella. John Finnerty and colleagues describe their approach to collection rearing, spawning and regeneration (doi:10.1038/nprot.2013.044)2, Isolation of DNA, RNA and proteins (doi:10.1038/nprot.2012.151)3, and characterization of RNA and protein expression (doi:10.1038/nprot.2013.014)4. To complete the quartet, Mark Martindale explains how his lab approaches overexpression and knockdown studies in this versatile beastie (doi:10.1038/nprot.2013.009)5.

We are hoping that this collection of protocols will provide a useful resource for aspiring cnidarian biologists. We would also be keen to see anyone with experience of working with Nematostella presenting their own protocols in the Protocol Exchange. The cluster also raises the following question:

Are there other emerging model organisms that are crying out for similar attention?

References:

1. Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization”. Science 317, 86–94 (2007).

2. Stefanik, D. J., Lauren E Friedman, L. E. & Finnerty, J. R. Collecting, rearing, spawning and inducing regeneration of the starlet sea anemone, Nematostella vectensis. Nature Protocols 8, 916-923 (2013).

3. Stefanik, D. J., Wolenski, F. S., Friedman, L. E., Gilmore T. D. & Finnerty,  J. R. Isolation of DNA, RNA and protein from the starlet sea anemone Nematostella vectensis. Nature Protocols 8, 892–899 (2013).

4. Wolenski, F.S., Layden, M. J., Martindale, M. Q., Gilmore, T. D. & Finnerty, J. R. Characterizing the spatiotemporal expression of RNAs and proteins in the starlet sea anemone, Nematostella vectensis. Nature Protocols 8, 900-915 (2013).

5. Layden, M. J., Röttinger, E., Wolenski, F. S., Gilmore, T. D. & Martindale, M. Q. Microinjection of mRNA or morpholinos for reverse genetic analysis in the starlet sea anemone, Nematostella vectensis. Nature Protocols 8, 924-934 (2013).

Antibodypedia on Facebook

Those readers who are avid, or even obsessive, followers of Nature’s various blogs will know that NPG is collaborating with a website called Antibodypedia since December of 2011. Well, last week we passed a significant milestone with the listing of its half-millionth antibody. And this week we are launching a Facebook page.

Antibodypedia attempts to pull together information about the performance of publicly available antibodies so that researchers can make informed decisions about which will work best in their experiments before they buy them. The data we aggregate are things like links to research papers in which the antibodies have been used, technical data from the antibody suppliers, and the results of experiments performed by independent scientists.

Antibodypedia is a great resource as it is, but the aggregation and presentation of information already available, albeit in diverse places, is only half of the story. We want it to also be a place where researchers can share their experiences with specific antibodies and discuss the problems that arise with immuno-based cell biology techniques.

We already have a mechanism in place for researchers to submit experiments showing the performance of antibodies, and an advisory board to help us peer-review those experiments to ensure their usefulness; it is a form of micro-publication. Now we are taking a further step in engaging with the research community with our Facebook page.

Why Facebook?

Well, it would have been perfectly possible to incorporate a message board, discussion forums and the other functionalities of a community site into Antibodypedia but the plain fact is the vast majority of researchers are already members of a global social networking site, so why ask them to join another one? Instead we are making things easy and carving out a small corner of Facebook for all things antibody(pedia). We will of course be posting a lot ourselves on the page—news, highlighting of research papers, running polls etc.— but we also hope that antibody-using researchers will start their own discussions, share their experiences and try to solve each other’s problems.

The page launches today so please come, take a look and ‘like’ us. Then come back regularly over the next few weeks to follow our posts, take part in the polls and, of course, leave a comment or two.

The Season of the Impact Factor

It is that time of year again! A bit like Christmas, now is the time when journal editors wait expectantly to open their presents; or in this case present singular. I’m talking about the annual release of Impact Factors from ISI. I’m not going to go through all the reasons why Impact Factors may not be the best way to judge scientific research. Katharine made some comments about that last year and I haven’t changed my opinion much since I railed against their tyranny at another journal. But Impact Factors and the other citation metrics probably say something about a journal so I thought I’d give you the numbers for Nature Protocols and say what I’m taking from them.

A picture from the cover

My favourite cover image from 2011.

So the 2011 Impact Factor for Nature Protocols is 9.924 which I’m really happy about. It would be a presentable number for a journal publishing primary research, and we don’t publish primary research. I would expect protocols to be formally cited less often. Also it is up 1.562 points from the 2010 value so Nature Protocols is probably being cited more than 12 months ago and hopefully that is an indication that our articles are being used more than 12 months ago. If our articles are being used more than they were then that’s good news.

Impact Factors are quite good for making comparisons between similar journals, but sadly none of the other main publishers of protocols is indexed by ISI and so don’t get given Impact Factors. I analysed the citation of those journals a few months ago and I’ll let you draw your own conclusions about what thier IF might be if they were given one. What ISI does do is put Nature Protocols in a group of journals publishing “Biochemical Research Methods”. Our colleagues at Nature Methods top that list with an IF of 19.276. However it is a bit like comparing chalk and cheese as other journals in this group are things like Acta Crystallographica Section D: Biological Crystallography (IF 12.619), Current Opinion in Biotechnology (IF 7.711) and even PLoS Computational Biology (IF 5.215). Still in the group we rank third, up from fourth last year, so again pleasing.

The numbers that please me are those that suggest that Nature Protocols articles have some longevity. If you calculate IF over 5 years instead of 2 it rises to 10.201 suggesting that Protocols are relevant well beyond their initial publication. Many journals, possibly even most (I’m eyeballing rather than having done a proper analysis)  have a lower 5-year IF than their standard 2-year IF.

For a slightly more sophisticated measure there is the Eigen Factor score. This is calculated in a similar way to Google’s page rank algorithm in that not all links are of equal value and self citations aren’t counted at all.  For 2011 ours is 0.10716. I’m not completely clear how to interpret that but it is more than for 2010 so that must be good!

Last up the Article Influence Score. This is derived from the Eigen Factor and then normalised for the size of the journal so that the ‘average’ journal will have an Influence of 1.000. Ours for 2011 is 4.422 which is again more than it was last year and shows, to misquote the immortal Yogi, that we are “smarter than the average journal (Boo-Boo)”.

So it’s all good (for as much as Impact Factors and similar measures can tell you anything about a journal).  But at Nature Protocols we don’t really care about the value of our IF. In the next 12 months we will try to commission and publish even better protocols so that more scientists will be helped in their research. If someone can quantify that then I’d like to hear about it.

The first few months of Antibodypedia

This is a guest blog post from Victoria Newman, the Antibodypedia curator.

Late last December I wrote a blog post for Stepwise announcing the launch of the new NPG resource Antibodypedia | nature (www.antibodypedia.com), an open-access platform to search for antibody data and commentary. I’ll talk more about what we’re trying to do below; however, as a quick status update, since our launch we’ve been steadily adding antibodies and making improvements here and there and have had lots of positive feedback from users. Most impressively, since the New Year we’ve been accessed from 136 countries, with repeat visitors from 113 countries in the last four weeks. Yay for open-access! But we know there is always room for change and we value your comments. Send us your feedback or, if you’re planning on attending the FASEB Experimental Biology (ASBMB) meeting next week in San Diego, stop by the NPG booth and let me know what you think in person: I’ll be there from 12-3 on the afternoon of Monday the 23rd.

So what does Antibodypedia do? We think of it as a microjournal, publishing bite-sized bits of data rather than full-length manuscripts. The data are specific to assays involving antibodies, since we believe that there’s huge scope for improvement with regard to their annotation—the process of buying them can be intensely chaotic, sometimes with very little information available to suggest that one reagent works better than another in the experiment you’re trying to plan. Our aim is to provide data from the antibody user community (including published references citing reagents) and antibody vendors or distributors to give users as well-rounded as possible a grasp of how a product works for different techniques. Because we feel strongly that your data (the control experiments in your lab notebook that may make it into supplementary data or may never see the light of day again) are the best way to convince other users that reagents do or don’t work, we’ve arranged to assign a DOI to each data submission so they can be cited onward. They don’t have to look lovely, especially if you think they’re evidence that something isn’t working, but we feel that they should be made public to help you troubleshoot your blank western blot. So send us your data—help users to answer the eternal question ‘Did I forget to induce my cultures again?’.

Advanced Search on Antibodypedia

Advanced Search

Because we want to provide researchers with the capacity to identify antibodies proven to work in specific techniques, Antibodypedia is structured slightly differently from many of the antibody search engines you might find out there: its organization is gene-centric, so each antibody directed against a single protein target can be retrieved by a search for that antigen. ‘Advanced search’ lets you find antibodies that are recommended or validated for one or more types of experiment, sold by a particular provider, and linked to reference citations, among other things. The ‘Advanced search’ menu is always undergoing development, so please let us know if it’s missing something you’d find useful.

 

After you’ve defined and run your search, your results will be displayed as a table, with each row representing a single antibody.

Search Results

Search Results

Clicking on a reagent will take you to antibody pages, which host or link to both user- and provider-sourced data as well as protocols and published references using those reagents.

Antibody Details

Antibody Details

You can also choose some of the antibodies retrieved by your search for side-by-side comparison to decide more easily which one(s) you’d like to test. Our antibody pages link directly out to vendor pages as well so you can find pricing and ordering information.

We think Antibodypedia will simplify selecting an antibody for a particular experiment by making quality control data both accessible to bench scientists and easy to interpret. But in order to maximize our utility, we need your help. Tell us which antibody providers you’d like to see listed in Antibodypedia so we can contact them and which techniques you use that aren’t currently searchable so we can start gathering data for them. And most importantly: submit to us so that we can populate antibody entries with your results! Remember that we’re not asking for publication-quality images, just something that can be interpreted as positive or negative proof that something’s working along with some notes on how you set up your experiment. Help us create an efficient means to search for good antibodies so you and your colleagues can plan your assays with less waste of time and money.

Blowing our own trumpet

As the sharp eyed among you might have noticed, Nature Protocols is running an ad campaign at the moment. If you haven’t here is one of our banners:

With this campaign we are offering anyone the opportunity of a month’s access to Nature Protocols. There are no catches other than that we want to know who you are, that we will send you an email after your month is up (which you can cheerfully ignore if you wish) to ask what you thought of the journal and prompting you to recommend us to your institution’s library, and that you will need to create an account for yourself on nature.com (which is also free). For that you can spend a month happily exploring the entire archive of Nature Protocols content.

Anyway, in the ads we are making a very specific claim: that nature Protocols is the most referenced source for protocols. A bold claim which I think I should justify here.

Normally when journals want to talk about their citations they turn to the Impact Factors calculated by ISI. That’s fine in the main, if you treat that number with some caution and only use it to compare very similar journals covering similar topics. Nature Protocols had an IF of 8.4 for 2010 (the most recent number) which we are very happy with although we hope that the number for 2011 (released in June 2012) will be a little higher.

However, laboratory protocols are useful long past the two year window from the year of publication that IFs consider. We could look at a 5-year impact factor (also 8.4 although higher if you believe in accuracy to more decimal places, which I don’t) which would be better, but the fact is that ISI don’t index or calculate IFs for the other publishers of research protocols: Current Protocols, Cold Spring Harbor Protocols, or Springer’s Methods In … series; and those are the people we would like to compare ourselves against.

So I had to do the calculating myself using the Scopus database of citations maintained by Elsevier. Using that I looked at all the papers published by Nature Protocols and our big three rivals from 2006, when Nature Protocols launched, to the present (well January this year when I did the number crunching anyway). I looked at every citation to any paper classified as ‘Article’ or ‘Review’. I also restricted the “Methods In …” series to research in the biological and biomedical subject areas. These are the data I got:

 

Published since 2006 Nature Protocols Current Protocols Cold Spring Harbor Methods in …
Total Number  1,474  1,859  1,090  1,0791
Total Cited  1,351  793  742  5,672
Total Citations  34,586  2,687  2,154  23,246
Average Citation Per Article  23.46  1.45  1.98  2.15
Average Citation per Cited Article  25.60  3.39  2.90  4.10
Highest citation  1,311  71  14  309
No in top 100 cited  91  1  0  8

As you can imagine that is very pleasing. Even if you mistrust simple means for a distribution that is far from Normal, Nature Protocols as a whole has been cited more than any of our competitors, and that despite publishing a much lesser number of Protocols than “Methods in…”. (I would say we are more selective but I feel I’m already crowing too much). And this isn’t due to one or two exceptionally highly cited protocols. It is true that one protocol* has been cited over 1300 times—1,533 times as of today—but of the 100 best cited protocols in this period from these sources 91 of them were published in Nature Protocols.

So there is the justification. Nature Protocols protocols are cited more often, and so presumably used more often, than any others.

* Da Wei Huang, Brad T Sherman & Richard A LempickiSystematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols 4, 44-57 (2009) doi:10.1038/nprot.2008.211