Archive for the ‘Science’ Category

I’ve crossed the following post at Denim & TweedThe science gender gap gets personal with #MyGenderGap, from which I’ve decided to steal the title. I’ve no twitter account yet (is that a fail? More and more academics are using it, but apparently biologists do poorly so this is just because!), so the only way to deal with the issue is to go blog about it.

The issue is about bias in gender in Academia. There’s been occasionnal mention to this issue here at SA (e.g. Gender & publishing), though just passing by (I’m not in a position to create new views, arguments or meaningful analyses on that matter, and there are plenty places where such things are produced or discussed so I usually get away with providing links).

It is all about a recent comment in Nature, which I’ll quote:

Thanks to Anne Jefferson on Twitter, I see that Alex Bond has called our collective attention to Nature’s great feature on gender equity in the sciences by making the whole thing as personal as possible: asking people to total up their collaborators and see what female-to-male ratio they find(…)

I’ll go more personnal below, but before, just have a look at their interesting map (it is just below if you don’t happen to have access to the journal): some countries just perform much better in term of women inclusiveness in science publication world:

Skewed gender in published research.

I don’t have field work pictures as Jeremy does, but it’s also true that most of my field times are rather lone or with reduced crews. Much of my previous work doesn’t strictly rely on field work but includes various lab steps, so I’m still able to crunch magic numbers about female to male ratios from my different work experiences past.

When I first counted collaborators (just including people with whom I published), raw numbers are 14 women and 7 men (that would be 8 if I count myself). So basically the sex ratio is 2.00 for my collaborators (1.75 if I collaborate with myself :) that should count since I’ve already published a single author paper).

That’s rather huge, compared to the USA average of 0.43 Jeremy noted (EDIT: 0.50 in France, but my work experiences are both in Fr & USA). But that’s because I’ve mainly worked in female biased labs throughout my early career. (it’d be interesting to keep track of the numbers as I currently work at a place where potential authorship should have a reversed trend –I should care about it clearly…)

At first, I investigated the numbers with counts on each paper, which yields a slightly different picture, since people are counted several times. My first ratio was 1.37 and I wondered why it differed from co-author ratio (which was 2.00). Then I realised I counted myself on papers but not in the collaborator sample. So when I drop myself from the papers, the ratio is 3.25 (that’s because I published regularly with the same female colleagues).

Whatever the calculation, I’m always in an atypical situation.

Of course I’m not discovering this: I already knew my work experience differs from most scientists because the basic or average place is biased toward strong maleness while my own path only crossed the reversed situation. Though I have to say that I happened to realise it only because people discuss the issue of gender bias (thanks internets! It’s never been discussed at workplaces). It never crossed my minds how outstanding my professional situation was before I read about this gender issue in Academia. But there’s something weird about this. I don’t know whether it’s telling something or pure luck is involved: if the common situation is a male dominated  Lab or Team, why did I never experience it (over 6 different work settings)? Is there anything that prevented me to work at the average Lab place? If so, we clearly all need some more awareness that there’s an issue, and it’s not getting away fast enough…

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You may find interesting consequences of megajournal open access journals (that’s impressive in term of numbers):

Open Access MegaJournals – Have They Changed Everything?

And this talk shared there: Open Access MegaJournals.

Certainly there’s been a change in the science publication ecosystem (that’s obvious). Unsure as to whether some aspects are easily documented, though:

- actual replication is accepted, but is it easy to find out which studies stand as replications from earlier works?

- “minor results” may indeed have found a way in the available “results pool”, but how do you say? It was clearly an issue prior to open access, since reviewers could reject on the basis that results were not interesting (whatever that meant), but OA doesn’t delineate between results unfairly rejected on spurious motives and “minor results”. Weren’t citation fate of papers telling us about fanciness already? (and not scaling on interestingness anyway!)

Did you ever get the feeling that these two aspects were saved by OA in specific cases? I haven’t yet. Which doesn’t mean it isn’t happening (I’m only saying it doesn’t read well even between lines). Or was I already swimming and reading in the pool of “forgotten studies”?

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In August, I presented a poster at ESEB 14th (biannual meeting of the European Society for Evolutionary Biology), that took place in Lisboa, Portugal. (ESEB was not especially commented upon by bloggers, maybe coverage was greater with other social media though… Anyway, you may find a few posts, there, there or there).

ESEB was apparently already known for its poster sessions… Just so you know.

Poster sessions this year were huge… I was breathing out with the latest genetics experiment (it was already 6 months old, but that’s still young to go to a science symposium). Maybe I was experiencing “poster solitude“. Indeed, people were’nt really staying that long. Maybe this is not a year to work on local dispersal, or maybe pathogenic fungi are just boring study models…

So, I always left readers stay, say, 10 seconds before I would show up and ask if there was any question. Safe bet, for 10 seconds is about the time needed to evaluate self interest in a random poster. Then, I got one attendee that stood up my own treshold. (I might even write swamped, because the time I went by it was probably already worth 20 seconds reading). “If you have any question…”, I enquired softly. But all I got back was a “Oh, I was just pretending!”. And she moved away.

This is the weirdest comment I ever had about a poster. Did it already happen to you?

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The quote this week:

Just as the alchemist yearned for a formula that would turn lead into gold, so the modern biologist longs for a conceptual framework that will make any data set coruscate with revelations. The framework described here falls considerably short of such expectations, but then, modern chemistry has not fulfilled the alchemists’ most ardent dreams.
S. J. Arnold (1983, p. 357).

From the following paper:

J. G. Kingsolver and R. B. Huey (2003). Introduction: The Evolution of Morphology, Performance, and Fitness. Integr. Comp. Biol. 43 (3): 361-366. doi: 10.1093/icb/43.3.361

is also the introduction from a special issue covering many interesting aspects of measuring natural selection. Seems like it is mostly open access, so I can link for you to go & pick on these various examples.

Then we can discuss the relevance of introducing path analyses to the study of natural selection in the wild: was it gold? I’d tend to think it was.

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A science videornal!

Just learnt about a new science journal whose standard format is video.

Incidentally, the journal’s name is Journal of Visualized Experiments (JoVE).

The reason why I didn’t know about this journal is of course that it’s not in my research field, indeed, it is far away, even stellarly (it is featuring mostly medical, chemical and physical research in a video format, and they write biology but I guess it is more like a molecular biochem thing –I haven’t browsed deep yet).


They seek to set a brand new publication standard (even if videos are part of publications since some time now, though I’ve never came to read a paper with videos in annexes.

Among the journal’s aims:

- Rapid Knowledge Transfer

- Addressing Complexity

- Lifting the Laboratory Time Sink

- Integrating Time

- Be a Part of a New Movement in Science Publishing

Sure they provide a new way to expose science, and it really looks like like they succeeded because they already have substancial amount of videos. But does the format really translate into either goals? Not if the scientist is not already a video geek I guess. And how would one give a thorough communication of evidence? We need access to analyses and estimate data quality and the like (does this format ease detailing stats enough?). How does it work this way? Unsure whether the video format would fit Ecology and Evolution studies. Oh yeah, go and browse, the videos are mounted as sections were you can make it fit the space, hopefully in substance… I can’t say more, as I actually don’t have access to this journal.

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Leaking News Factory

This week in ecologies & evolutions:

  • Free living (not viling) eucaryotes species can last a long time (over a decade!) under hard drought conditions, without being specifically adapted to dryness or flood (when it happens). Calls for inherent resilience of [Australian] semi-arid floodplain soil communities under increasing pressure from climatic induced changes in water availability. Soils probably suit for enduring changes, which is good news.
    Baldwin D S, Colloff M J, Rees G N, Chariton A A, Watson G O, Court L N, Hartley D M, Morgan M j, King A J, Wilson J S, Hodda M, Hardy C M (2013). Impacts of inundation and drought on eukaryote biodiversity in semi-arid floodplain soils. Molecular Ecology 1365-294X DOI: http://dx.doi.org/10.1111/mec.12190
  • Traditional experiments on pathogen growth curves relied on air temperature. This study suggests we better use leaf temperature instead. Certainly will lead to arrays of follow ups…
    Bernard F, Sache I, Suffert F, Chelle M (2013). The development of a foliar fungal pathogen does react to leaf temperature! New Phytologist 1469-8137


  • This wins the funny title, as it may be misleading by jargonry. The “ecosystem engineer” plays a key role in food webs, being a common foodstuff for a number of marine birds including the oystercatcher. Hope you didn’t want to apply for the job. Climate change will alter ecosystem functionning, and has begun to impact the spawning period in the cockle, which extended over a greater number of months compared with previous studies.
    Morgan E, O’ Riordan R M, Culloty S C (2013). Climate change impacts on potential recruitment in an ecosystem engineer. Ecology and Evolution 2045-7758 http://dx.doi.org/10.1002/ece3.419

And that’s it for this week.


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Troubles deciding where submitting your manuscript? The discussion was initiated from this post at Dynamic Ecology, so it’s also even more interesting to Seeds Aside in that it’s fully in the ecological sciences. Much has been said already, I have to let you read many reactions at various places and comments there.

Since I’m probably transitioning in my own takes on these points, I’ll split my take between past and possible future change. (more…)

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Bioquote otw #3

This week’s quote is not from a paper or a book, but directly from a blog post. You can find the whole text there, it is discussing the future of a recent ecological journal, Ecosphere, and it is an interesting take on a specific review process that may enroot in Academic publishing soon, “Cascade Reviews“.

Here’s the quote:

Perhaps your review process experience is always smooth sailing, but many of us are spending a lot of time revising and resubmitting papers that are technically sound but that reviewers dislike because they don’t like the topic or are uncomfortable with the take home message, or (my favorite) this isn’t the paper that they would have written themselves.

Hum, Academia. I think the quote is self explanatory. Sometimes your studies are approaching that almost* final stage, being published. But it does take many steps, the review process is not the easiest one. There are sometimes reasons for the review to derail, most of the time it has to do with uncareful reviewers, especially when they thought they could handle the review but eventually lacked time for proper appreciation of the work and ended up reading too fast or uncautiously or relied on really prime feelings about it.


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Here we are:

  • Old rural parks support higher biodiversity than forest remnants. That is, because they are at least much higher with large-diameter dead wood types, which increases diversity mediated by big wood chunks.

    K Lõhmus & J Liira (2013). Old rural parks support higher biodiversity than forest remnants. Basic and Applied Ecology   http://dx.doi.org/10.1016/j.baae.2012.12.009

  • The Technological favourite: Functional genomics of a generalist parasitic plant: Laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression. Certainly a prowess, spotting gene expression patterns at a very very local scale (cells). And the model plant parasite modulates expression depending on host encountered… Wow!

    LA Honaas, EK Wafula, Z Yang, JP Der, NJ Wickett, NS Altman, CG Taylor, JI Yoder, MP Timko, JH Westwood & CW dePamphilis (2013) Functional genomics of a generalist parasitic plant: Laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression. BMC Plant Biology 2013, 13:9 doi:10.1186/1471-2229-13-9 (open access!)

  • Title says it all: Tropics accelerate the evolution of hybrid males sterility in Drosophila. If this finding can be generalized a bit, then it lays out a process to tropics species higher diversity.

    R Yukilevich (2013). Tropics accelerate the evolution of hybrid males sterility in Drosophila. Evolution   DOI: 10.1111/evo.12056

  • A dating success story: genomes and fossils converge on placental mammal origins. Good news, sometimes hard stones evidence and molecular clocks agree at finer scale!

    A Goswami (2013). A dating success story: genomes and fossils converge on placental mammal origins. EvoDevo DOI: 10.1186/2041-9139-3-18 %T (open access!)

  • Title price: funny edition: The elephant in the room: the role of failed invasions in understanding invasion biology. That is for conclusion marketting! And indeed, there’s room to reflect upon failed invasions, because many studies of invasives try to correlate success with characteristics (we aim to predictability of invasions!).

    RD Zenni & MA Nuñez (2013). The elephant in the room: the role of failed invasions in understanding invasion biology. OIKOS DOI: 10.1111/j.1600-0706.2012.00254.x

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Just because it sounded too good not to mention it. A taxonomy of coauthor species.

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