Friday links: scooped by a blog post, the real history of P-values, lab safety, and more

Also this week: the history of #icanhazpdf, microbiome pet peeves, new evidence of widepread p-hacking, the difference between terrestrial and marine ecologists, using software to solve the wrong problem, and more. Oh, and never mess with a manatee.

From Meg:

Jacquelyn Gill has a post that provides an important reminder about the importance of considering lab safety. Fortunately, no one in my lab has had an accident as serious as hers, but someone did cut her hand (while making chemostats) enough to require an immediate trip to the doctor. As a grad student, I had to drive a student to urgent care after she sliced her foot open on something while wading into a lake in a limnology class. I sliced my own foot on a zebra mussel in a different lake. And when I worked as a technician between college and grad school, the other tech had what initially appeared to be a very, very bad cut to her hand, but that fortunately ended up not being very serious. So, it’s clear to me that things can go wrong and, combine that with me being the child of a nurse and a fireman (safety first!), and you’d think my lab would be all about the safety training. But Jacquelyn’s post has me realizing that I probably haven’t thought about this enough. We have some basic safety measures (especially that people should head into the field with a buddy, that you need to get off the lake at the first sign of a thunderstorm, and that no one is allowed to go out in the boat unless they can swim); at Georgia Tech I made sure everyone in the lab knew the number to call if there was an emergency and had this taped to the lab phones. (It wasn’t 911 because that would get Atlanta police, whereas GT police would be able to respond faster.) But how would people respond in a situation like the one the Gill Lab was in? I’m not sure. Then again, what sort of training could we do that would prepare folks for the wide variety of (fortunately unlikely!) situations that could arise? Definitely lots to think about!

On twitter, people use the #icanhazpdf hashtag to ask for pdfs that they can’t get on their own (usually via institutional access). For people at institutions, this is a way to bypass the InterLibrary Loan (ILL) system (and I think often results in getting a pdf more quickly). This paper has an interesting summary of #icanhazpdf, including its history and information on what is being requested. It also includes this depressing sentence:

The current scholarly publishing system is so broken that some researchers are forced to make requests like “Still looking for a pdf of my own paper! Please help.”

From Jeremy:

Sociologist Andrew Lindner on how a paper of his was scooped by a blog post, and what this says about the scholarly publishing system. I wouldn’t overgeneralize from what seems like an unusual coincidence, but still, interesting to think about. (ht Brad DeLong)

Noah Fierer’s pet peeves of microbiome studies.

The potted history of P-values, at least when told by certain sorts of Bayesians, is that they were an invention of R. A. Fisher that set scientific inference on the wrong basis for the better part of a century. For instance, Nate Silver spends a whole chapter on this potted history in his recent book. Statistician Stephen Senn corrects the historical record (emphasis in original):

Fisher did not persuade scientists to calculate P-values rather than Bayesian posterior probabilities; he persuaded them that the probabilities that they were already calculating and interpreting as posterior probabilities relied for this interpretation on a doubtful assumption. He proposed to replace this interpretation with one that did not rely on the assumption.

The upshot, Senn argues, is that Bayesians don’t really have a problem with P-values. Rather, they have a problem with other Bayesians. And many contemporary complaints about the evils of P-values are misdiagnosing the root of the problem. Go read and then join the (already lengthy!) discussion in the comments.

Marine ecologists are organism/system focused, terrestrial ecologists are question-focused. At least, that’s one way to interpret the fact that marine papers name the study organism(s) much earlier in the introduction than do terrestrial papers (Menguia & Ojanguren 2015, open access). Casey terHorst comments. Meg, what do you think the results would be if you looked at freshwater ecology? (ht @hughes_lab)

Head et al. 2015  (open access) text mined all open access papers on PubMed and examined the distribution of P-values <0.05 to look for evidence of p-hacking. It’s a very careful study, more careful than most of casual text mining on this topic that I’ve linked to in the past (somewhat to my regret). Turns out p-hacking is widespread across scientific disciplines covered by PubMed. The results also suggest that scientists mostly are studying real effects rather than chasing noise. Head et al. also found evidence of p-hacking in meta-analyses of sexual selection in evolutionary biology, but not enough to dramatically alter the conclusions of the meta-analyses.

A while back we did a post on ecologists who are awesome at things besides ecology. In the same spirit, I give you Ravens offensive lineman John Urschel, who is a serious mathematician. (ht Marginal Revolution)

Straight from the horse’s mouth: the relationship between academic economics and economics blogging. (ht Marginal Revolution)

This week in Treating the Symptom Not the Disease: dude, if you need software to tell you if a scientific paper was computer generated, your journal has problems no software can fix.

And finally, never mess with a manatee.🙂

10 thoughts on “Friday links: scooped by a blog post, the real history of P-values, lab safety, and more

  1. “Marine ecologists are organism/system focused, terrestrial ecologists are question-focused. At least, that’s one way to interpret the fact that marine papers name the study organism(s) much earlier in the introduction than do terrestrial papers.”

    I do have a different (possible) interpretation. I think most terrestrial ecologists are just as focused on their organisms or their systems, but there is a greater pressure in the scientific community of terrestrial ecologists to generalize as much as possible. If you specify your site/organisms too early, you’ll get dinged for not being of broader interest to the readership. Perhaps it’s just that marine people own the fact that a lot of biology is system-specific and they trust other scientists to evaluate the broad applications for themselves.

    • I agree with this view. It’s a cultural trend and I was explicitly taught to frame my research in terms of larger issues and not species or sites. Most everyone I know is super into their study organisms* and more rarely sites** but if you asked them about their research foci, they would say it’s landscape ecology, or nutrient cycling, or evolution, or however they are framing it these days. I also have to say that I think this issue is getting negative. I have run into some papers that have some broad topic title and upon reading the paper, I realize it’s actually not as broad as it seems. For example, one paper title was about a weird passerine behaviour but it turned out to be about crows which are not typical passerines and the behaviour was not surprising if only applied to crows.

      I recently ran across an article about how often papers are cited across marine, terrestrial, and freshwater systems that might be interesting to people. Terrestrial ecologists ignore aquatic literature: Asymmetry in citation breadth in
      ecological publications and implications for generality and progress in ecology. Menge et al. 2009. Journal of Experimental Marine Biology and Ecology.

      *birds, herps, and fish people – we are crazy about our study animals. Our offices are decorated with photos and paintings. We have pictures of us holding them. I know people who have named pets and kids after their study animals. And we all just write issues papers. Mammal people are probably the same way but I oddly don’t work with a lot of them.
      **tropical and Arctic/Antarctic people especially

  2. The issue of lab and field safety can never be taken too seriously, and at times is something not even considered by PIs. I witnessed, and experienced nothing short of a colossal debacle concerning environmental health & safety, and labor law during a three-year period on a particular project. So severe were these problems that there were frequent outbreaks of infectious disease (girardiasis, food poisoning) because the PI never bothered to provide safeguards for working in remote locales. At one point, we were dispatched to a region engulfed in wildfire. Even after two study sites were incinerated, and daily warnings were given to the PI, no accommodations were provided. We inhaled a dangerously toxic atmosphere for 5 full days, with no protective gear. None of us had any training to cope with wildfire. I was even ordered to continue working with food poisoning, and not allowed to seek out medical assistance, due to fears of the PI that insufficient grant funds existed to conduct an additional trip for data acquisition. I could go on, but I will spare you additional detail on what was a plethora of statutory infractions.

    In the wake of this Three Stooges retrospective, I was motivated to investigate what, if any standards existed concerning work in remote field locations. What I found was that plenty of guidance… and regulations… and statues are already in place. In Colorado, the legislature codified into law (1961, I believe) upwards of 150 or so standards regarding employee health & safety in remote locations. As you might well imagine, the PI on the project I mentioned violated just about every one of them. When I investigated what was applied by the private sector (primarily environmental consulting firms in the US)- I found that almost universally they applied the rules and regulations adopted by the US Army for troop deployment (whether real or training-related) to remote locations. I also discovered most firms require their employees to be trained & certified in first aid (not the one-day training version, but 3 month course) and remote country search & rescue. I was fortunate to have had paramedic training in my youth, and that has benefited me and others throughout my life. Once during field work in the 1980s, I rescued a young lady from drowning & applied CPR. Without that training, she would have perished.

    It is also really very important that supervisors/ PIs develop well-thought emergency plans in advance of deploying personnel to remote locations. Where are the available escape routes? How do you contact local authorities for help? What if there is no cell phone signal? What if vehicles break down or roads become impassable? Where is the nearest medical clinic or hospital. Does the local sheriff have the GPS coordinates of your camp? When developing these plans, PIs should assume anything that can go wrong will.

    An ounce of prevention, when it comes to working in remote locations, is more than worth the pounds of grief you shall spend trying to repair that which cannot be repaired after the fact.

  3. Hi Jeremy, I’m a “marine ecologist” for what that’s worth. My impression is that marine vs. terrestrial ecologists focus on different (eco)systems, with different questions – however using ecological tools and thinking to understand how organisms relate and interact with each other and their environment.

    That said, as in most fields, I am fairly specialized with a focus on marine microbial organisms aka: plankton. I would like to comment that aquatic sciences (freshwater and marine) could benefit from more fluent discussions with their terrestrial/field ecology counterparts with respect to common themes in their research questions. The apparent trend towards organism-driven vs. question-driven research may be a by-product of the rapid tools available to aquatic scientists which enable genomic level understanding of organisms to facilitate IBMs. I’ll comment only that having an individual-based understanding of an organism allows marine/freshwater aquatic ecologists to expand to population level questions which is data intensive given the dimensionality of scale. Perhaps it comes down to a – small are many, and the large are few(er) problem.

    • Interesting perspective, thanks. Although IBMs are kind of the next big thing in terrestrial plant ecology too, so perhaps the apparent trend here will go away before too long…

      • What’s IBM? It is here qualified as the next big thing so we need to know!🙂

      • Individual-based models. Although actually I had a brain cramp in my previous comment–I think I*P*Ms are the next big thing in terrestrial plant ecology. IPMs are integral projection models.

  4. Casey wrote, “At the Benthic Ecology meetings, where nearly all talks are about marine organisms, talks often start by discussing the study organism on the first slide, whereas at the Ecological Society of America, talks begin with a broad discussion of ecological theory and the study organisms pops up around slide 5 or so.”
    I think the traditional take on ASLO talks is the same as what Casey describes for Benthics — organism introduced early (maybe on the first slide). But I think that has shifted somewhat (though I haven’t been to ASLO in several years at this point). But, yes, I would write a pretty different introduction for a paper I planned to submit to Ecology vs. one that I would submit to L&O, even if it was the exact same study (and I consider those both to be very good journals.)

    His next sentence is:
    “You see this at NSF too, where the Population and Community Ecological panels at DEB are focused on ecological questions, but the Biological Oceanography panels tend to focus more on study system. Even the ecologists in our own department at CSUN are divided into two sections: Marine Biology and Ecology & Evolution.”
    This is different, because freshwater ecologists would go in to PCE, too, so the proposals are generally written similarly to terrestrial proposals.

  5. H Jeremy and Casey, thanks for picking up the paper. I would encourage people to read it (it is open access) and discuss it. We were just trying to generate awaress about the issue. When I presented these data at the Benthic Ecology Meeting, there was a surprisingly large backlash amongst the audience. While the issue may seem academic, it has very strong ramifications into general education, funding and government agency structures (e.g., parks, EPA, USGS in the U.S.).

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