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Science pubs and bling

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How many research papers are, from the conception, just bling?

Bling, you say? From the Urban dictionary:

The word "bling" refers to any unnecessary accumulation of metal or jewellery which impresses the simple-minded. Examples of bling-related activity include: driving a car with shiny platinum rims, arriving at a movie premiere in a hat made of glittering diamonds, or pointing at a big block of gold and cooing away for hours on end like an unforgivable moron whose mere existence ultimately cheapens us all. Bling is the single most shallow, boring and wilfully superficial cultural phenomenon ever to excite humankind, which is saying something for a species already hooked on internet poker.

Einstein, math, genius and strange people

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From Nature News (paywalled as far as I know), Steve Hsu's comments are here

Entrepreneur’s ‘Project Einstein’ taps 400 top academics for their DNA

He founded two genetic-sequencing companies and sold them for hundreds of millions of dollars. He helped to sequence the genomes of a Neanderthal man and James Watson, who co-discovered DNA’s double helix. Now, entrepreneur Jonathan Rothberg has set his sights on another milestone: finding the genes that underlie mathematical genius.

Rothberg and physicist Max Tegmark, who is based at the Massachusetts Institute of Technology in Cambridge, have enrolled about 400 mathematicians and theoretical physicists from top-ranked US universities in a study dubbed ‘Project Einstein’. They plan to sequence the participants’ genomes using the Ion Torrent machine that Rothberg developed.

I like his attitude, a little bit less his calculations:

Rothberg is pushing ahead. “I’m not at all concerned about the critics,” he says, adding that he does not think such rare genetic traits could be useful in selecting for smarter babies. Influenced by a college class he took from a pioneer in artificial intelligence, and by the diagnosis of his daughter with tuberous sclerosis complex, a disease that can cause mental retardation and autism, Rothberg has long been interested in cognition. He is also in awe of the abilities of famous scientists. “Einstein said ‘the most incomprehensible thing about the Universe is that it is comprehensible’,” he says. “I’d love to find the genes that make the Universe comprehensible.”

[...]

Project Einstein “is unlikely to have any statistical power”, says geneticist Daniel MacArthur at Massachusetts General Hospital in Boston who, with colleagues, has amassed a pedigree of 13 million related people to try to tackle the heritability of complex traits (see Naturehttp://doi.org/ppj; 2013)

Here for the strange people:

Others say they wouldn’t be surprised if the study found that maths aptitude was not born so much as made. “I feel that the notion of ‘talent’ may be overrated,” says Michael Hutchings, a mathematician also at Berkeley. He adds that even if genetic markers are found, they could be used for good — not to pre-select for maths geniuses, but to help parents to understand the particular abilities of their children and give them the support they need.

The fact that talent does not exist is pathetic lie and it is ever more pathetic when it is coming from someone who is clearly talented. I think that some people will never jump over political correctness (or so called PC, since I do not see how saying that some people in specific fields or across certain fields are more talented than others might be not respectful of people. I am clearly enormously less talented than LeBron James for playing hoops. Should I feel less worthy when someone is pointing that out? I do not think so).

Rothberg is adamant that the project is well worth the time and the money, whoever is paying for it. “This study may not work at all,” he says — before adding, quickly, that it “is not a crazy thing to do”. For a multimillionaire with time on his hands, that seems to be justification enough.

It should be.

Papers I am "reading"

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When there is no volume/pages, it means it is in press ("in press" apparently still not supported by Mendeley)

Bateson, P., and K. N. Laland. 2013. Tinbergen’s four questions: an appreciation and an update. Trends in Ecology & Evolution.

Benyshek, D. C. 2013. The “early life” origins of obesity-related health disorders: New discoveries regarding the intergenerational transmission of developmentally programmed traits in the global cardiometabolic health crisis. American Journal of Physical Anthropology.

Berg, O. K., G. Bremset, M. Puffer, and K. Hanssen. 2013. Selective segregation in intraspecific competition between juvenile Atlantic salmon ( Salmo salar ) and brown trout (Salmo trutta). Ecology of Freshwater Fish.

Christiansen, F., G. a. Víkingsson, M. H. Rasmussen, and D. Lusseau. 2013. Female body condition affects foetal growth in a capital breeding mysticete. Functional Ecology.

Correia, D. 2013. F**k Jared Diamond. Capitalism Nature Socialism.

Ellegren, H. 2013. Genome sequencing and population genomics in non-model organisms. Trends in Ecology & Evolution.

Emery Thompson, M. 2013. Comparative Reproductive Energetics of Human and Nonhuman Primates. Annual Review of Anthropology 42:287–304.

French, W. E., B. Vondracek, L. C. Ferrington, J. C. Finlay, and D. J. Dieterman. 2013. Winter feeding, growth and condition of brown trout Salmo trutta in a groundwater-dominated stream. Journal of Freshwater Ecology 1–14.

Goto, A., H. Arioka, and R. Yokoyama. 2013. Plastic life-history variation along the course of a steep mountainous river in male Cottus hangiongensis (Pisces: Cottidae). Environmental Biology of Fishes.

Lanfear, R., H. Kokko, and A. Eyre-Walker. 2013. Population size and the rate of evolution. Trends in Ecology & Evolution.

Marcil-Ferland, D., M. Festa-Bianchet, A. M. Martin, and F. Pelletier. 2013. Despite Catch-Up, Prolonged Growth Has Detrimental Fitness Consequences in a Long-Lived Vertebrate. The American Naturalist .

Marks, J. 2013. The Nature/Culture of Genetic Facts*. Annual Review of Anthropology 42:247–267.

Moorad, J. A. 2013. Individual fitness and phenotypic selection in age-structured populations with constant growth rates List. Ecology.

Nelson, R. M., M. E. Pettersson, and O. Carlborg. 2013. A century after Fisher: time for a new paradigm in quantitative genetics. Trends in Genetics.

Robinson, O. J., N. H. Fefferman, and J. L. Lockwood. 2013. How to effectively manage invasive predators to protect their native prey. Biological Conservation 165:146–153.

Skolnick, A. M. H., A. Moroni, E. Siri, and L. Soliani. 1973. A Reconstruction of Historical Persons from the Parish Registers of Parma Valley , Italy. Genus 29:103–155. (related to a project I am working on and I will describe at some point)

Stier, A., V. a. Viblanc, S. Massemin-Challet, Y. Handrich, S. Zahn, E. R. Rojas, C. Saraux, et al. 2013. Starting with a handicap: phenotypic differences between early- and late-born king penguin chicks and their survival correlates. Functional Ecology.

 

When I read amazon reviews, I read the one-star reviews first

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I read Amazon reviews, especially on books, every day, often multiple times a day. I love reading and I love (very often) reading other people's opinion on books. I always start reading the one-star or two-star reviews. Why? Well, I guess because when someone is strongly against something, I want to know why they are. Was the book boring? Inaccurate? A pathetic attempt? Or the lonely one-star review was making reference to Kindle formatting or late delivery? It happens pretty often.

After having read one- and two-star reviews, I jump to three-star ones. They are often the most informative. Who is giving three stars? I know I am generalizing, but very often (I read and I am interested largely in non-fiction) it is some guy with deep knowledge of the topic, with an opinion, who can find strong and weak points , and for whom a three-star book is a book worth reading, with some caveats. Five-star reviewers are usually fans, and I do not care that much about fans' opinions.

Herbert Gintis is one of my favorite reviewers.

Answering to reviewers

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How to answer to reviewers' points, suggestions, comments, rants etc. is something I consider every time I have to answer to reviewers, points, suggestions, comments, and especially rants. The Italian school, as far as I know, is on the very polite side of the fence. You start by writing:

We thank the Editor, Associate Editor, reviewers for the very interesting points, comments and suggestions (not rants) that will surely improve the new version of the manuscript. We are grateful for the possibility of resubmitting the paper (actually we would have preferred a major revision, but apparently the way of the Tao in the last 5 years is rejecting everything and then with some benevolence allowing a resubmission, which is not a guarantee of future consideration and absolutely not of future publication, since as stated in the bottom of the mail coming from the Editor, just before the signature, only 10 to 20% of the submitted manuscripts are getting published in this very selective journal because even in 2013 there is competition for space) and we answered in detail to each and every question, comment, suggestion, point raised by Editor, Associate Editor and reviewers. Thanks a lot again".

Then, in the actual "Response to Reviewers" you start the answers to reviewers' points (90% of the time), with "We perfectly agree with the reviewers" or "We understand reviewer's concern". Which, by the way, is true most of the time. When it is not true you write it anyway because looking for battles when they allowed you out of benevolence to submit a greatly revised version of the manuscript (because the previous one was totally unacceptable and also the Editor agreed with the reviewers) is not the way forward.

Now, how do I like authors to answer to my points when I am reviewing their papers? Do I care about how they answer (dear reviewer, thanks for your brilliant consideration) or only to what they answer (i.e. content)? Well, I'd say that I am much more interested in what they answer with respect to how they answer if how they answer is acceptable. I am very elastic and so far I never had any concerns. I am much more interested in science than in formalism. So, why am I paying more attention than other scientists (given my experience) on how I answer? Does it make a difference? It should not, but.

New paper submitted

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I submitted a new paper (aka tour de force) with title "Determining individual variation in growth and its implication for life history and population processes using the Empirical Bayes method" that is the result of a collaboration between myself, Marc Mangel, Hans Skaug, Steve Munch and Alain Crivelli. Four nations (Italy, US, Norway and France), multiple projects, one paper.

Here is the 200-word abstract:

The differences in demographic and life-history processes between organisms living in the same population have important consequences for ecological and evolutionary dynamics. Modern statistical and computational methods allow the investigation of individual and shared (among homogeneous groups) determinants of the observed variation.

We use an Empirical Bayes approach to estimate individual and shared variation in somatic growth with a random-effects model. As a case study, we consider two populations of marble trout Salmo marmoratus living in Slovenian streams, where individually‑tagged fish have been sampled for more than 15 years. We introduce cohort and density during the first year of life as potential predictors of the von Bertalanffy growth function’s parameters k and in addition to the individual random effects.

Our results showed that size ranks were largely maintained throughout lifetime in both populations. The best models according to the Akaike Information Criterion showed different growth patterns for year of birth cohorts as well as the existence of substantial individual variation in growth trajectories after accounting for the cohort effect. Model predictions of individual growth trajectories were largely more accurate than predictions based on mean size-at-age of fish. We consider both the life history origins of these patterns and their implications.

You can find data, code and a preprint on figshare. To run the code you need to install ADMB (I used version 11) and R. I think the total line of codes are between 5 and 10 thousand. It has been a long work (aka tour de force) and not-soon-to-be repeated.

NSF reviews and grade inflation

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I just completed a review for the NSF on a very interesting proposal in the ecological, population biology etc. area. Probably because I am foreign national, this is the first time (maybe the second and the first time I declined?) I was asked to provide a review. After completing my summary I had to choose the final grade. I thought Very Good was the right grade because they were a couple of things that needed to be addresses, but I remembered what John Boyd was saying about "grades" in the army, where being merely excellent meant not being suitable for promotion. "Colonel is excellent in every aspect" meant between the lines that the Colonel was getting sacked. You needed to be super or ultra excellent in every aspect and more. Boyd is an interesting read by the way, although apparently his influence in the military has been in the neighborhood of nothing ("folk hero" has been the definition of someone in the know). One time I also took inspiration from his analysis and synthesis dual approach to learning and understanding for my teaching statement in a job application, but apparently the committee thought I was merely excellent and not super excellent. Now that I remember (refresher here) Boyd was also very very weird, so maybe taking inspiration from his bizarre views was not a good strategy. Better in any case than being boring (remember than interesting is better than boring and fun is better than not fun, although right is most of the time better than wrong and this may create conflicts with the fun part) with all the "my mission in life is teaching undergrads and please give me a job and I will teach 4 courses each quarter (give me a job is the lynchpin, by the way)". So, I might propose again the analysis/synthesis destruction/creation dual approach, just for the fun of it (and I also believe it is an interesting approach, at least it was at the time). I will tell you how it goes. By the way, I enjoying teaching undergrads.

Getting back to grades, I googled online and I came across this 3 years old post from the popular Female Professor blog. After reading that Very Good is not actually very good, but, meh, kinda good, I bumped my grade to Excellent since I believe that the proposal should get funded. Be aware fellow reviewers that what you write should reflect what you think as well as what they think you are thinking. Since you do not know what they are thinking, bumping up might be generally a good strategy. At least, that was my choice.

New photos of Slovenian sampling "ops"

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Check out the photo section of the website, I have just added some fantastic photos of marble trout sampling "special ops" going back to 1993. It is amazing that the same guys are still sampling the same streams with the same enthusiasm, skills and passion after 20 years. Great job guys (click on the photo for a larger version).

Sampling in Volaja, 1993

Sampling in Volaja, 1993

Gorska, 2005

Gorska, 2005

upvol05-0023

Upper Volaja, 2005

Update on Research

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From last week:

  • Paper needing revision for Journal of Fish Biology. I received quite general reviews, in some places very general comments with very little attention to results. Since the modeling is quite complex and the statistical analyses quite detailed, I would have appreciated much more attention to those parts. The paper deals with the consequences of massive mortality events , think floods, wildfires, rain-on-snow, on evolution of traits (in particular body growth and age at sexual maturity) and on population dynamics of affected fish populations. The results are interesting, there are consequences on the evolution of traits, albeit of small magnitude with respect to simulations where traits are not allowed to evolve, but very little consequences on population dynamics and risk of extinction. So, there is evolution, but in term of consequences at the higher level (population), nothing to write home about. This has consequences also when thinking about fishery-induced evolution of traits. One of the reviewers is asking for more generality (you never go wrong asking for more generality, yes we are talking about floods, but you need to write that you are also talking about oxygen crisis, poison, oil spills, divine intervention, basically everything that can generate a strong response. I believe floods are not general enough, since they unfortunately kill people, kill fish and other animals, cause billion of dollars of damage every year all over the world etc.). Other requests are connections to conservation measures (not much unfortunately, floods are just a common occurrence, especially in mountain streams) and other stuff on the "minor" side.
  • Received request for moderate revision of a paper submitted to Hydrobiologia. Doable, I should stress more the novelty of my approach and clarify the use of water velocity as a predictor for suitability of habitat for the growth of a clam of great commercial value. It is an area of research I am not actively pursuing, but I enjoy giving answers to very applied questions. I have a wide range of interests, and how to solve "real" problems is one of them. However, I do not know I will continue working in this area or not. I'd enjoy write another paper on the use of ensembles to better predict the distribution of species of commercial value. The idea is there and the algorithm has been partially developed, the problem is as always time and focus. This is the abstract of the paper:

    "Species distribution models are still scarcely applied for the estimation of potential productivity of aquaculture species. Here, we show how a simple species distribution model can be used for the rapid estimation of commercial yield potential and for the identification of suitable sites for Tapes philippinarum in two North Adriatic lagoons. We use a two-part species distribution model with sediment type, hydrodynamism, dissolved oxygen and salinity as predictors. The first component of the model uses logistic regression to identify the areas in which clams occurs or not, while the second component estimates the potential yield (kg m-2) by applying a  weighted geometric mean  of suitability values. We estimate the weights  of the geometric mean with site-specific yield data  by a constrained linear regression, validate the model on independent data and then apply the two-part conditional model to the whole surfaces of the two lagoons. The model provides a good prediction of the yield data in the validation dataset (R2adj = 0.86). The calibration and application of a simple HSM  model can be a useful tool for objectively identifying the most suitable sites for aquaculture activities and support the sustainable management of farming activities in the Po river delta."

    I plan to send the ms back to Hydrobiologia in a couple of weeks. I need also to redraw a figure and I will test my skills with Adobe Illustrator, just for fun.

  • I am almost ready to submit with my colleagues the manuscript on the estimation of parameters of parameter-rich von Bertalanffy growth curve functions using the Empirical Bayes method as implemented in ADMB. Lots of code, lots of figures, lots of testing. I learned a lot, but it took a lot of time. The problem now is setting the introduction properly. It is not easy, as the ms has the aim of providing both a "novel" method and new biological insights on the growth process. The methods has been applied to a couple of populations of marble trout, and it generated some very interesting results on the shared (think about year class effects) and individual (genetic + stochasticity, like finding a good spot for foraging) determinants of the observed variation in growth trajectories. In about a week at most, I will submit the paper to American Naturalist.
  • I submitted almost a couple a months ago to American Naturalist my solo paper on the evolution of a quantitative trait following extreme events, and since the 24th of September is waiting for American Naturalist's Assistant Editor and Editor decision. I am waiting too.