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Open Access or not

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Very interesting discussion on Twitter today that started after someone said that she was not considering open access (OA) publications as an outlet for her (apparently) top material. Michael Eisen, PLoS co-founder, accused her of hypocrisy and the discussion started. For me at this point is a no-brainer. In Ecology and Evolution (as a discipline, it is also the title of a OA journal, the poor sister of Evolution) after PLoS Biology there is a lack of option of OA journals with high impact factor or rank or credibility. Ecology and Evolution is (basically) the OA option for papers that have been rejected by Evolution (review cascade, yes, sure. We do not want your paper in our prestigious journal, but you can pay $1500 and get it published in our much less relevant journal), PLoS One for papers that have been rejected at least a couple of times by more relevant journals (PNAS, rejected --> Ecology Letters, rejected --> American Naturalist, rejected --> ok I am fed up, let's go PLoS One, accepted. Just ask), EcoSphere is for papers rejected by Ecology, Ecological Applications, Frontiers etc. For sure there are scientists submitting to those OA publications as first option, but the vast majority submit there because they have been rejected between one and multiple times by other journals. For a journal to become relevant takes some time. To build credibility takes some time.

Grant agencies want the Nature, Science, PNAS publications (and higher PLoS journals, sure), they want publications in top disciplinary journals (AmNat, Ecology Letters, Ecology, ARES, Trends in Ecology and Evolution). Look here for the publications of ERC winners, how can that be not clear? Do you see any Ecosphere? PLoS One? Ecology and Evolution? Is it so difficult to understand?

People publish only OA out of an ethical position. I respect that and I am ethically in favor of OA. I'll maybe follow in a few years.

Aside: Marissa Mayer, Yahoo!, and being pretty annoying

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If you have one hour of your time sitting there for you, and going to beach, playing with your kids, drink something etc. does not seem a good option, I recommend this Business Insider's article on Marissa Mayer. Super-driven, clearly very smart, so far her Yahoo! tenure has been a huge success (but read how Alibaba must be partially responsible), but there is a but. Quite a few buts, actually. Would I enjoy working under her? Not at all. Always late, she tries to out-talk you, very often she cancels one-on-one meeting without previous notice and no justifications, makes people wait for her forever, no social skills, she says that raising baby is easy when she has an army of helpers, nannies, a $5 million penthouse, come on.

"Mayer had approximately 25 people reporting directly to her during her first year at Yahoo. In theory, she was keeping up with each of them in a regularly scheduled weekly meeting. In practice, she would go weeks without talking to people because she was so busy.

For a while, each of those 25 people thought that Mayer was just picking on them, individually. The people who had been at Yahoo before Mayer joined assumed that this meant she was going to fire them soon. The people Mayer had just hired into the company, including Reses and Savitt, were even more puzzled. Why had they been hired only to be ignored?"

I like analytical people, I don't enjoy that much the "slap in the back" attitude, especially when I am on the receiving side of slapping, I am all for talking shop up to 2am and  getting back at it after 3 hours of sleep, but cancelling appointments like the other guy is worth neither your "I am sorry" nor some kind of explanation, having open office hours like you are an high school teacher, well, I think I'd last 10 minutes. A lot of people left Yahoo! after she got the CEO position, and apart from business and personality clashes inevitably happening at that level, a lot of decent people I believe simply couldn't put up with the disrespectful behavior and attitude.

I do not believe there are "success" lessons in the Mayer's story. Luck makes a huge difference in people's lives and thinking that the road to work or business success can be algorithmically explained or predicted is naive at best. Smart, hard working, brilliant people are on average (and there is a threshold effect for some of those traits, simply people who are not smart in a loose and broad sense are very unlikely to be successful, although we often associate smartness to quantitative and mathematical skills and intuition, and it is quite limiting) more likely to succeed than less smart, less brilliant and lazier people, but beyond that everything is really context-specific and hugely dependent on being at the right place at the right time. Looking at success stories backwards sometimes gives clues, a lot of times doing that is very misleading. The Success Equation is a good read here.

The article, although quite verbose at times, gives a solid and interesting picture of how business deals (including getting a new CEO on board at Yahoo!) are made at the highest level. Very interesting and highly recommended.

ESEB meeting recap

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The ESEB meeting left me quite satisfied, although the proportion of talks I really liked was probably ~ 1 out of 5. I think that the submission of abstract 6 months in advance is partially responsible of some sub-par talks. Some of the talks were about papers that I already read and were published in 2012 or in early 2013 and I do not see the point of listening to a talk about a paper I already read. Some of the talks were about ideas only partially developed, and you could tell it.

The plenary by Trudy Mackay about the genotype-phenotype mapping in Drosophila made me think pretty hard. If in a model (the model) species like Drosophila (with more ~ 200 inbred lines) predictions at the individual level for polygenic traits using SNPs are far from being acceptable (she vigorously supports the idea that epistatic interactions are responsible from the lack of predictive ability from simple additivity), do we have any chance of making right now or in the foreseeable future half-decent predictions for polygenic traits in non-model species? We are very far from it, although Craig Primmer was able to predict correctly 8 out of 10 times the age at sexual maturity in Atlantic salmon using SNPs outliers from a GWAS association study.

Here below, the talks I listened to at the European Society of Evolutionary Biology meeting in Lisbon, 19-24 August 2013. 32 talks total.

Tuesday 20th Aug 2013

De-Meaux: The molecular underpinnings of adaptation in Arabidopsis Thaliana

Ellers: A new perspective in phenotypic plasticity

Foray: Can we predict the effect of thermal fluctuations on specialist and generalist reaction norms?

Morrissey: Selection and evolution of causally-covaryint traits

Duthie: A fluctuating environment drives coexistence in five non-pollinating fig wasps

Reed: Quantifying the demographic cost of selection in a changing environment

Wednesday 21st Aug 2013

Hoglund: Why genetics, genomics, bioniformatics and evolutionary theory may matter for conservation

Geroldinger: The influence of the genetic architecture of a trait on local adaptation in a subdivided population

Chevin: Evolution of discrete phenotypes from continuous reaction norms

Bernatchez: Applied evolutionary genomics in fish conservation: some success stories and challenges for the future

Primmer: A GWAS association study of age at maturity in Atlantic Salmon: implications for conservation and management

De-Cara: Maintaining fitness and diversity in conservation programmes

Otto: Genomic scope of adaptive mutations to different environments

Thursday 22nd Aug 2013

Greaves: Cancer through the eye of evolutionary medicine

Danchin: Genetic and nongenetic inheritance

Friday 23rd August 2013

Mackay: Charting the genotype-phenotype map: lessons from Drosophila

Stearns: Comparing phenotypic, quantitative genetic, and genomic approaches to measuring tradeoffs in a contemporary human population

Hoyle: The fitness implications of adaptation via phenotypic plasticity and maternal effects

Tarka: Evolutionary potential of arrival date on breeding grounds: selection, heritability and microevolution

Whitlock: Equilibrium and non-equilibrium demographic history and the distribution of Fst

Richards: Epigenetic response to novel and changing environments

Fox: Demographic heterogeneity, selection, and population response

Nitsch: Sibship effects on dispersal behaviour

Kvalnes: Estimating fluctuating selection in age-structured populations

Wensink: Indicators of selection pressure and changes in vital rates at multiple ages

Saturday 24th Aug 2013

Lummaa: Sex differences in natural selection on reproductive scheduling and longevity in humans

Coulson: Using evolutionary demography to link evolution and ecology

Chantepie: Actuarial senescence increases the risk of extinction of mammal populations

Lohr: Reduced lifespan and increased ageing driven by genetic drift in small populations

Butlin: Reinforcement

FitzJohn: What drives biological diversification?

Hoekstra: Sexual something (title had symbols, but it was about evolution of sex)

 

What I am reading

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The Sports Gene by Epstein

As a guy who has been involved in sports all his life, I am as certain as a scientist can be (that is, not 100%, but very close) that there are intrinsic differences in sports abilities. It is not only the early environment, not only the social environment, not only motivation or grit or persistence (which, by the way, as behavioral traits should be heritable. That means that there is an "environmental" and a "genetic" component). Looking forward to reading this book.

On getting more efficient - part 1

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I thought a lot lately about how to get more efficient at what I do (I hate wasting time and getting side-tracked), and I am going to write a series of posts presenting my workflow, find tons of holes in it as well as finding/testing way to get more efficient.

One of most compelling reasons to go to meetings and workshop is to take some time off from your routine, listening to some folks and get encouraged or discouraged or neutral, try to convince people that your way is the way, and think about what you can do to improve (in a broad sense) your research program, which ends up most of the times to find better and easiest way to publish in top journals and getting cited a lot. No solving world problems or getting a profit here.

I am right now working on 3 model systems (if I remember well, hint: problem), many different topics within the same model systems (including theory), and I expect things to get messier quite soon when I will get the genetic data from marble trout (a month or two, the sequencer just arrived at the lab). I am not teaching and I am quite limited administrative work. Two group meetings a week lasting 1 to 2.5 hrs each. (At least) Part of the weekend (almost always) on.

I am satisfied by my production of ideas and code on a daily basis, including writing a blog post around 5am in a Lisbon hotel because I am jet lagged. I typically work on a one or two model systems a day with a switch that gets quite "formal" most of the time (e.g. I open another workspace in R), and within the same system I typically in a single day on one or two problems. For example, I may work in the same day on kittiwakes (1st model system) and on marble trout (2nd model system). For kittiwakes, I might work on testing measures of growth variability and their effects on survival and reproduction, and for marble trout I might work on estimating the repeatability of body size and on estimating the standard error of parameters on the random effect effect model of growth I am currently working on (2 problems). Plus, for each model system/problem, I typically produce an amazing number of plots, since I am very keen on visual communication to myself and other people. Should I focus on one single problem a day/a week, the same problem for the model system each day/week until solved and ready to get shipped? Or more interesting/fun to work on many problems/model systems at the same time trusting your supernatural abilities of concentration while worrying about the fact that things very clear right now are clear a mud next week (advice to myself: comment code a lot more)?