Friday links: the Great Emu War, world’s oldest bar graph, 10 principles of ecology, and more (UPDATED)

Also this week: compile ALL the p-values, grad students vs. abuses of power, Michael Phelps vs. pumpkinseed sunfish, p-hacking with covariates, one year’s worth of data = two year’s worth of data, a canonical R gotcha, and more. Including a contest to win 1000 Internet Points, and links from Brian!

From Jeremy:

William Playfair: inventor of the line graph, the bar graph, and the pie chart. Click through for cool pictures of some of the world’s oldest graphs. (ht Marginal Revolution)

Interesting potted history of algebra, calculus, and their effect on physics. Calculus as the “killer app” of algebra. Also the point that progress in physics often consists of reinterpretations of the same equations. (ht @noahpinion)

Ecology grad students often feel a strong urge to collect a second year’s worth of data, or data from a second site, or a second species, or etc. Stephen Heard argues that that’s usually pointless–or it would be except for the fact that reviewers often like to see it.

Econometrician Marc Bellemare comments on recent work on p-hacking with covariates in economics and political science. Equally relevant to ecology, and easily accessible to ecologists. If you’re ever going to run a general(ized) linear model in which some of your predictor variables are covariates intended as “control variables”, you should read this post and have a look at the papers discussed therein. (ht Economist’s View) Relatedly: Andrew Gelman points out that, in a hierarchical model, adding a predictor can increase the residual variance. Keep that in mind if you’re trying to use proportion of variance explained by a variable as a measure of its “importance”. Gelman also reminds us that, in a hierarchical model of observational data, the effects of an individual-level predictor and its group-level mean cannot be straightforwardly interpreted as “direct” and “contextual” effects, respectively, even if the data are a random sample from the population of interest.

Speaking of p-hacking…Simply Statistics graphs the distributions of published p-values in each of many scientific and social scientific fields. In every field except one, the distribution is strongly bimodal, with one peak at very low p-values and a second peak centered just below 0.05. In the exceptional field, published p-values have a unimodal distribution centered on very low p-values. +1000 Internet Points to the first commenter who can name the exceptional field without peeking. πŸ™‚ No it’s not physics. And no, it’s not “ecology, evolution, and earth sciences” either, though in that field the second peak around 0.05 is relatively small compared to its size in most other fields. You may also be interested depressed horrified interdepressified to learn that the distribution of published p-values in “complementary and alternative medicine” looks like the distributions for most other fields.

Terry McGlynn shares some data showing that preprints might be taking off in biology (specifically, on bioArxiv). Terry explains why he’s not jumping on the preprint train, at least not yet, while also saying that he doesn’t think his reasons should be anyone else’s. I’d say the same as Terry. Do what works for you. And here’s a counterpoint to Terry’s post. UPDATE: And here’s Manu Saunders’ counterpoint to the counterpoint. Includes the completely unsurprising observation that the vast majority of ecology preprints on PeerJ and bioArxiv had received even a single peer comment, none had more than two, and the few comments there were were not nearly as substantial as typical peer reviews at decent journals. It’s totally fine if you want to post your preprints in the hopes of getting substantial feedback. But you’re very unlikely to get it. And if you do get it, that makes you very unusual. More data here reinforcing Manu’s observation.

A canonical R gotcha: the colon operator takes precedence over arithmetical operators. I just ran afoul of this one and resorted to emailing Ben Bolker in desperation when I couldn’t figure out why the hell my code wasn’t working.

Australia: the only country in history to lose a war to birds. (ht @noahpinion)

It’s David Shiffman’s favorite week of the year! For some value of “favorite”. πŸ™‚ Ok, the question of whether Michael Phelps can beat a great white shark in a swimming race is silly clickbait. Especially since you have to simulate the race, because the actual race would look like this. Here’s a more interesting and fun question: what’s the biggest fish Michael Phelps could beat in a 100 m swimming race? Obviously he can’t beat a great white shark, but equally obviously he could beat a dwarf goby. So where’s the crossover point? I’m guessing something smaller than a trout? I would totally watch Michael Phelps race, like, a pumpkinseed sunfish. Bonus: Phelps and the sunfish could actually race safely; it wouldn’t have to be a bogus simulated race. C’mon, let’s have #pumpkinseedsunfishweek! In the comments, please share your suggestions on the best fish for Michael Phelps to race, along with your rationale. Thread winner gets +1000 Internet Points. πŸ™‚

I assume the problem was Zen Faulkes’ luggage. πŸ™‚ (ht @matt_levine)

From Brian:

Here is a very thoughtful group of graduate students taking on all forms of abuse of the strong academic hierarchy (starting from a sexual harassment incident) in a very wise and constructive fashion starting with department-wide conversations. Check out the resource tab on the above linked web page to see what they implemented at their home university. Seriously, if you want to do something about these problems check out what they’re doing. If you are interested in learning more about how you could extend this to your university they have a workshop Tuesday evening at ESA.

Mike Kaspari is boldly listing the 10 fundamental principles of ecology to organize his teaching. Read it for the science to see if you agree with his list, or read it to think about how this approach can help organize your teaching (Meghan conducted a similar exercise for intro bio).

17 thoughts on “Friday links: the Great Emu War, world’s oldest bar graph, 10 principles of ecology, and more (UPDATED)

  1. As a life-long distance swimmer, I can say there is no better non-sensual physical activity to be had! Swimming rules, dude. It is the singular most beneficial exercise available to us. Case in point: heart disease is rampant on both sides of my family. In 2015, at age 53, my heart was subjected to months of intense medical evaluation for an unknown condition that had afflicted me.

    The physician called me one day and said, “We had to dig deeply through 100+ years of hospital records, but as far as we can tell, you are the only patient we ever had that has an absolutely perfect heart. It’s unbelievable- I’ve never seen anything like it, especially in a man your age.”

    So I dug into the literature looking for a possible explanation, given my family history. I found one: primates that engage in over-the-head exercise with their arms experience virtually no incidence of heart disease. Hence, my life-long love of swimming seems to have spared me the family illness.

    The obvious answer to a Micheal Phelps losing contestant would be the woefully pathetic seahorse. It swims like a brick. But I must be honest, Jeremy, you’ve disappointed me in overlooking the obvious candidate: a Daphnia specimen from Meghan’s lab!

  2. On preprints: One advantage that was (surprisingly) not considered in neither of the three linked pieces: many journals are now integrating preprint servers into their submission process (called “direct transfer” at biorxiv, journals already participating include Science, PNAS, Oecologia, J Exp Biol). This means, that you don’t need to upload a ms two or three times if it is desk rejected at the first journal, rather you upload once to the preprint server and then every 1st submission to a new journal is (almost only) one additional click. Some journals in the molecular sciences have also started to actively look for preprints and invite them to be submitted and peer-reviewed. If this would be adopted widely it would potentially save a lot of time in the whole process.
    see here
    https://blogs.biomedcentral.com/on-biology/2016/12/14/ahead-of-the-curve-embracing-preprints/
    and here
    http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006448

    • “Some journals in the molecular sciences have also started to actively look for preprints and invite them to be submitted and peer-reviewed.”

      Interesting! Is it selective journals that are doing this, or just author-pays open access journals like Plos One, that reject few papers and survive on publication fees? And if it’s selective journals, do you know anything further about how they pick the invitees? Are editors actually reading the preprints carefully and evaluating them? Looking for the rare preprints that get lots of comments or retweets? Or is it more like a presubmission inquiry at someplace like Nature, where some combination of the author’s name recognition and an interesting-sounding abstract is enough to get your foot in the door? The linked articles give a few details, but I’d be very curious to know more.

      It’s interesting to imagine the dynamics of publishing in a hypothetical future world in which journals competitively “bid” for what are in their eyes the “best” draft mss. That world would be more efficient than ours in some ways, yes. But one wonders if it would also have downsides. For instance, if you’re worried about possible bias of peer review toward famous authors now, imagine how that bias would operate in a world in which journals identify preprints to bid on based on how many comments those preprints have received and how often they’ve been retweeted…

      • I don’t know much more than what is behind these two links and a couple of anecdotal reports I’ve seen on Twitter confirming these two pieces. Seems like a relatively new development.
        As for the standing of the journals: AFAIK Plos Genetics is a relatively selective journal.

      • Hard for me to imagine bidding. We don’t really have coin to bid with so our bidding would pretty much have to be impact factor (highest impact factor gets it) which would have to mean that bids would have to be guaranteed acceptance as best I can work out. And talk about over emphasizing impact factor. If I were having to bid with guaranteed acceptance (as it appears the law journals do), I would have to scrutinize a paper quite carefully – indeed since I am not an expert in most areas I would have to send things I was half way interested in out to review.

      • Presumably friar Gregor Mendel, for instance, would never have been published under such a scheme? Science does have a distinct beauty pageant flavor to it and so you are right that there are many instances of favored status in the publishing world. Fact is, I have time and again found research published ONLY as a thesis or dissertation that is some of the most amazing science I’ve ever read, and has very often contributed more to my work than ANYTHING ever published by a “top dog”. I would say Plos One is one step in the right direction, but the financial component needs to be reduced or eliminated so everyone can participate. I agree that moving toward any sort of bidding system would only amplify the negative aspects of the existing good ole boy network. Given the rapid advances in information technology, I think we are closer than ever before at eliminating the gatekeepers.

      • “I think we are closer than ever before at eliminating the gatekeepers.”

        Except that eliminating the gatekeepers doesn’t democratize anything. The distribution of attention paid to anything–books, movies, pop songs, scientific papers, you name it–is *very* highly skewed, always has been, and always will be. A small minority of stuff gets a large majority of the collective attention. And if you think the “crowd” is invariably wiser than, say, individual peer reviewers in deciding what’s worth paying attention to, be aware that by far the most viewed and downloaded ecology paper in Plos One’s history is about fellatio in bats (at least, it was last time I checked). Not kidding at all when I say that’s surely a fascinating natural historical topic. But come on: let’s not pretend that the “crowd” has demonstrated its superior science-evaluation skills. You think that reviewers for Nature, Science, or PNAS are biased in favor of “sexy” stuff that lacks lasting merit? Well, sex sells to the “crowd” at least as much.

        You want a democracy of attention? A world in which every paper gets an equal share (one paper, one unit of attention?). Or at least, has an equal *chance* at an equal share? The only way you get that is forcible redistribution of attention. Which is what pre-publication peer review is: forcible attention redistribution. Every submission that’s sent out for review gets the close attention of 2-3 people. It’s the only democratic (or nearly democratic) stage in the scientific publication process. It doesn’t produce equality of post-publication attention, and there’s no reason to expect it to. But at least it levels the playing field and gives every paper something resembling an equal shot.

        I don’t think I’ll ever understand anyone who argues that getting rid of gatekeepers is democratizing. The same bad argument was made at the dawn of the internet. We have the web now! Anyone can publish anything and be read by anyone! No need to get past those bad ol’ gatekeepers at the NY Times or wherever to get your words in front of millions! But yet, somehow only a few bloggers ended up with millions of readers and only a few Twitter users ended up with lots of followers, and for the most part the rest have approximately zero.

        As an aside, I’m actually fine with highly skewed distributions of attention, if only because I see no good way to avoid them. I just don’t like it when the existence of that skewed distribution is mistakenly attributed to evil, biased “gatekeepers”, with the idea that if only they were eliminated we’d have an attention democracy.

        Sorry for banging on. This is a hobby horse of mine.

      • No apologies necessary, Jeremy, as I agree with much of what you’ve said. I do not believe attention can or should be ‘democratized’. Reviewers as you say play a very crucial role as well. My use of the term ‘gatekeeper’ was in comparison to Plos One. While Plos One has minimum standards for publication, it does not exclude papers solely on the basis of author interpretations, or any other factor beyond experimental design and analysis. I would allege the gatekeeper concept is so very deeply embedded in our science culture that we seldom recognize it, and I am as guilty of that as anyone.

        Consider, for example, exhibit A: https://www.theatlantic.com/science/archive/2016/07/how-a-guy-from-a-montana-trailer-park-upturned-150-years-of-biology/491702/
        Toby Spribille had ZERO chance of becoming a scientist via a North American education. By the skin of his teeth he found a program in Germany. Recently, he’s become a sensation- and most deservedly so. There was no diabolical or sinister wizard at the gates of US education telling him to go away. That ‘wizard’ perished long ago, but the system he put in place remains. Toby was excluded from science by American universities.

        I am not alleging editors are diabolical or sinister, because as best I know they are not. But they too enforce a system that by design is exclusionary and in some cases, yes, unfairly so. My broader point which was not clearly articulated is that information technology has the potential to free us of these systematic constraints. We can still have peer review and whatnot, but we can also eliminate inherent biases with a democratized publishing system. One somewhat like Plos One, but that is essentially cost-free and implementing open peer review. Notice though I am not arguing for democratization of attention, only access if the methods and analyses are sound.

        Your example concerning the NYT is a great one, considering a slew of recent events in the US. The NYT has extensively covered the ongoing scandal concerning Russia intervention on the 2016 election… but, only very recently had a singular article concerning the scandal involving Representative Wasserman-Schultz and the theft of US Congress data and hard drives by Pakistanis working for her. The juicier story- the one selling newspapers, is about the president. But it is quite likely the more compelling story is the one where that facts and evidence are already known.

        I am not trying to lobby against what you are saying, Jeremy, but I do stand by my point that we should modernize our publishing system. I believe that is already happening and for the better.

      • There are whole web sites devoted to the world of ‘open access in publishing’ vs the world of traditional publishing [ aka, a gate keepers’ world]. See…http://www.thepassivevoice.com/ for a great one. Jeremy is quite correct about the lack of democracy in attention!

      • I appreciate the link, Eric. Yes, I have closely followed Jeremy’s previous posts on publishing-related topics, including open access publishing. Jeremy has provided wonderful insights to thee issues and raised awareness in a very important way. Please allow me to reiterate I am NOT arguing for democratization of attention. I never said that. I completely agree that our “participation ribbon” culture is a farce, and that yes, we live in a dog-eat-dog world. “Suck it up, buttercup” is my personal creed, for gosh sake! There are always more losers than winners, period.

        That said, I do not believe there is much point in arguing or debating the issue of the existence of open access all that much longer. Just as the Pony Express came and went, so too shall the current publishing system in science. I am not saying open access journals are problem-free, for they are not. I am not saying they are the be-all to end-all. I think we are all familiar with the scandals emerging from open access publication of fraudulent articles, in part facilitated by the editors of traditional journals… but, the frequency of fraudulent publications has lessened markedly in recent years. Obviously we also have issues with predatory open access journals, but I believe that problem is removed when financial/profit motives are eliminated. Open access publishing, like so many other things in the information age is evolving and adapting. But moreover, it is growing and the trend is an obvious one.

        From 2009 through 2015, open access journals more than doubled their numbers in the scholarly marketplace, and in 2013 already had a 12% share of the science journal market. Those numbers have leveled off somewhat in recent years, but growth continues. The main objections to open access are the occurrence of predatory journals, lack of adequate peer review and publication of junk science. These issues continue but I believe are being addressed, and that we are moving in a positive direction. I find the potential benefits of open access publishing to be remarkable. For those journals requiring little or no author fees, the upside is tremendous. Academia is great when it comes to chomping the gums about “workplace and academic diversity,” but so very often fails to put those principles into practice. And while I agree that women and ethnic minorities deserve inclusiveness in science and society as a whole, there is much more of the pie that is left out. Economic discrimination is rampant.

        There are 1.2 billion people living on less than $1.25 per day. Three billion people live on less than $2.50 per day. I am not saying open access publishing will cure world poverty, because it won’t. What I am saying, though, is that based upon these numbers alone, we can conclude that way more than half of the world’s population has no access to scientific publishing.

        Diversity in science? Are you kidding me?

    • Oh, that’s much better than my pumpkinseed sunfish joke! I would totally watch Michael Phelps race a sea otter.

      I’m slightly surprised to learn that Phelps would beat an Emperor penguin easily.

  3. Pingback: Friday links: what is the (dissertation) matrix, bidding for preprints, and more | Dynamic Ecology

  4. This is the first time I have got into this thread and I am struck by the amount of wining and dining and gender debates and animals only being mentioned as jokes. No wonder wildlife is in such a bad way!

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