Category: Blog Posts

First thoughts on SF DORA

First thoughts on SF DORA (https://am.ascb.org/dora/) The following was posted in The Node as a response to a call for comments on the SF Declaration of Research Assesment (https://thenode.biologists.com/san-francisco-declaration-on-research-assessment/news/) The declaration is a very important step forward to untangle the situation we have got ourselves into. However, the size and the direction of the step will be determined by how, who and how firmly the resolutions are implemented. Some habits are difficult to quit and one can see people not mentioning the impact factor (IF) explicitly but using it implicitly valuing publications in the same journals as a proxy for […]

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On ambition

In science ambition has always been understood as the intention to do something interesting, either by solving a difficult problem that will provide a general insight into the workings of Nature (gravity, the atomic structure of matter, evolution….) or to create something that will be generally useful (a microprocessor, a steam engine, the Golden Gate or the ability to perform in vitro fertilization). However, increasingly, at least in the life sciences, the term has adopted a new meaning: ‘where you want to publish’. You are ambitious if you want to publish in one of those journals that we shall call […]

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Orwell’s principle of Peer Review: all authors are equal in the eyes of the editors but in High Impact Factor journals, some Authors are more equal than others.

It happened again. Talking to someone about things of the trade: papers, publishing in the life sciences actually, happened to mention a piece of work I had just seen in Cell; “did that get published?….” my companion jumped…. “really?……..I rejected that work!….. but well, it is so-and-so and it is Cell…..”.  Indeed; the topic is what they call ‘hot’, the authors are well known in the field and, one presumes, the editors are easily impressed by names, trendy topics and technologies…….who cares about content or rigour: plus ca change…….peer review which for most of us is a complicated and treacherous […]

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Searching for the inner structure of biological systems; an ongoing quest

An address to PhD students from NIMR and UCL at Mill Hill (London, UK) 16 May 2013. There is pdf version of this post here.  “It is difficult and often impossible to judge the value of a problem correctly in advance; for the final award depends upon the gain which science obtains from the problem. Nevertheless we can ask whether there are general criteria which mark a good mathematical problem……. A mathematical problem should be difficult in order to entice us, yet not completely inaccessible, lest it mock at our efforts. It should be to us a guide post on […]

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Appendix to “What do genetic screens tell us about the inner structure of biological systems in developmental and cell biology”

Outline of a proposal for the inner structure of the cell: an interactive project. Here I would like to put forward a seed for a framework to think about the ‘inner structure of the cell” which should help framing the outcome of genetic screens. S. Brenner has talked about the inner representation of an organism when referring to the manner in which its different parts, its development are encoded in the genome. I would argue that in order for this notion to be useful and to be useful in the use of Genetics to unravel it (see the companion piece […]

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What do genetic screens tell us about the inner structure of biological systems in developmental and cell biology?

NOTE: This is not a review (this is not the place for such things). This is a commentary, a couple of rough notes unpolished and free in style, an attempt to generate discussion and debate, of pouring out some thoughts. One important thing,  in case you reach the end: I believe what I say here. It is likely that this will evolve. If you have any thoughts or comments, do not hesitate to contact me (ama11@hermes.cam.ac.uk). A PDF version of this can be downloaded from here. “We are confronted by a nonlinear system the theory of which is fragmentary, complex […]

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Chemistry, the missing link in “The Double Helix”

Last week there was a celebration of the 60th anniversary of the publication of the papers (sometimes it seems as if there was only one but, actually there were three) on the structure of DNA. The occasion invited recollection and reflection and, perhaps for the last time, allowed some of the protagonists to tell the world famous events in Cambridge, UK.  Much ink has been poured over this to the point that some times it does not feel like Science but rather like a fairy tale, a legend about a girl in the midst of boys chasing a structure which […]

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Can we think of something important to say?

The death of Francois Jacob (1920-2013) has triggered many deserved tributes and comments, as well as brought back the memories of a time and a place when Science was, different, certainly more focused and the realm of few. The first time I heard about Jacob was, of course, in the context of Jacob and Monod, in undergraduate Genetics in Madrid. This was a landmark moment as it showed me what Biology was capable of, that Biology could be beautiful, that one could find logic and order in what otherwise would be a mere collection of facts and that you can […]

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How to evaluate our output

It is very good to see that, slowly, the OA battle is being won. There are still a few rough edges to be smoothened out, particularly in the US, but the battle is being won and everybody is aware of the problem and the solutions. What is best, progress is being made. Now we can maybe turn on the heat on a situation which, probably, does not have an easy solution but which, increasingly is a cause of aggravation, intellectual discrimination and ……: the current mechanisms of peer review and the meaning and use of the Impact Factor (IF). I […]

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More about the current state of scientific publishing and how to start change

Additional observations Our lab has an ongoing fruitful collaboration with AK Hadjantonakis at the Developmental Biology division of MSKCC in New York (www.mskcc.org/research/lab/anna-katerina-hadjantonakis) and a recent visit coincided with the publication of an article from Leslie Vosshall on the current state of scientific publishing and the effect it has on careers and, overall, the field (www.fasebj.org/content/26/9/3589.full). Leslie kindly made time to see me and we had a good exchange during which we shared our views of the problem and ways towards solutions. She proposes some in her article by making a rational appeal to the common sense of authors, reviewers […]

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