Monthly Archives: June 2015

Journals of Irreproducible Research – downgrading reproducibility and fact checking

As far as I am concerned, good science is about communication and reproducibility, or, as Stephen Heard argues, at least being able to believe that it is reproducible.  I would argue a bit more strongly than Stephen, in that I think you should, at the very least, be able to be confident that you could reproduce the experiment without having to contact the author(s) and that you can also easily check the cited literature.   In this context, there are two things that really annoy me about some of the so-called ’high impact’ established print journals and their on-line would be rivals.  First, the way in which the methods and materials section is relegated to the end of the paper, often in smaller font, and in some cases to the supplementary material section  In other journals e.g. Nature, the methods section is also very minimal and I defy anyone to repeat those experiments!  My second bugbear is the habit that some journals have, possibly to reduce space, in making you use numbers to denote references, placing them either in parentheses or superscript in the main text.

Perhaps I am alone in this, but I do like to know whose work is being cited without having to constantly refer to the references section.  What  particularly annoys me, are those journals that not only insist on numbered references but then list them in number order and not in alphabetical order!  I once wrote a review paper for Annual Review of Entomology, which has the numbering system, but subverted it by listing my references alphabetically – the editor never noticed 😉

You may say that what all these journals are doing is merely structuring the paper in the order that people tend to read them which is, I admit, a valid point. To me however, they are saying to the scientific community, perhaps not overtly, but certainly subliminally, that methods and materials are something you don’t really need to bother about, somewhat akin to those things that you store in an attic or basement, just in case you might want them at some time in the future, but probably not often, if at all.

Hidden methods

This sends a strong and erroneous message to authors that despite the methodology being the most important part of how we do our science, as long as they report the general gist of how they did things it is fine.  To referees the subversion of the methods section sends an equally strong signal; you don’t really need to spend a lot of time reading about the methodology as long as the rationale for the work is justified and that the results are significant and well presented.

As someone who works on insect-plant interactions I constantly come across inadequate methods and materials sections both as a referee and as a reader of published work.  The thing that perhaps causes me the most annoyance are descriptions of plant phenology.   Herbivorous insects have a very intimate relationship with their host plants and the growth stage of their host plant or the age of the plant tissue that they are feeding on can have very marked effects on their development, survival and fecundity (Awmack & Leather, 2002).  I so often came across methods descriptions along the lines of “10 day-old cabbage seedling” “ 3 week old pepper plant”,  “2 week-old wheat plant”, that in desperation I wrote an editorial (Leather, 2010) explaining how important it was to use a measure that didn’t depend on the temperature,  photoperiod, nutrient or water status that the plants were grown at i.e. the BCCH scale.  I also compiled a virtual issue of Annals of Applied Biology, with relevant examples drawn from the journal which has a long and distinguished history in publishing such articles.  If you can’t find your host plant in past issues of the Annals you will find that most plants have a published version somewhere, even if only on Wikipedia.  Despite my efforts however, I still often have to remind authors to describe the phenological stage of their host plants accurately and precisely.

Methods and materials, please come back, we need you!

 

References

Awmack, C. S. & Leather, S. R. (2002). Host plant quality and fecundity in herbivorous insects. Annual Review of Entomology 47, 817-844.

Leather, S. R. (2010). Precise knowledge of plant growth stages enhances applied and pure research. Annals of Applied Biology 157, 159-161.

 

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Ten Papers that Shook My World – Owen & Weigert (1976) – The things that eat you are good for you

Journal clubs have been around a long time, but as a new PhD student in 1977 it was a new experience for me.  I was thus somewhat uncertain about what was expected from me when my supervisor presented me with a copy of Owen, D.F. & Wiegert, R.G. (1976) Do consumers maximise plant fitness? Oikos, 27, 488-492, and informed me that I was going to present my views on the paper the following month.  In those days organised PhD training programmes in the UK did not exist. Nowadays, PhD students in the UK follow a programme of lectures and workshops ranging from statistics, presentation skills, paper writing, ethics, use of social media, how to run tutorials, IPR, critical appraisal,  etc. etc. Given my lack of experience,  I was a little apprehensive to say the least.  Luckily I had the chance to see how the older members of our research group dealt with their papers in the preceding weeks and was somewhat moe confident about what was expected of me.  I duly read the paper and highlighted the areas that I wanted to critique.

O&W1O&W2O&W3

Parts of the Owen & Weigert (1976) paper showing the bits that I highlighted for my critique.

Owen & Weigert’s hypothesis was, that contrary to accepted doctrine, consumers, especially those feeding on trees, were beneficial to their host plants and not harmful.  Coming fresh from an agriculture department where I had been taught that anything that ate a plant was a pest, this was a startling and heretical concept for me to digest!  I remember at the time that I was not particularly convinced by the arguments and that within the group the general consensus was that Denis Owen was a bit of an eccentric.  In fact, the senior members of the group entered into a printed debate in the popular scientific press (McLean et al., 1977; Owen, 1977) which resulted in what I still consider to be the best ever front cover of New Scientist 😉

New Scientist cover

Arguably the best ever front cover of New Scientist

 We were not the only ones who expressed scepticism about Owen’s hypothesis, although experimental rebuttals of Owen’s claim that aphids and trees were in a mutualistic relationship via honeydew production did not appear until some years later (Petelle, 1980; Choudhury, 1984, 1985).  These papers resulted in a series of spirited responses from Owen (Owen & Wiegert, 1982a, b, 1985, 1987).  Some years later, however, Joy Belsky provided further evidence against Owen’s hypothesis (Belsky, 1986,1987; Belsky et al., 1993) and I too entered the fray (Leather, 1988,2000).

Thus by the end of the last century it appeared that all the evidence indicated that if you were a plant, being eaten was not good for you.  On the other hand, if Owen had posed his hypothesis at a population or group level, he might have been able to make a better case for herbivores increasing plant fitness. In an earlier post, in which I wrote about the plant immune response and how plants communicate with each other when attacked and warn their neighbours of potential attack, one could definitely make a stronger case for plants benefitting from being eaten.  Induced resistance can even work at an individual level, some recent work (McArt et al., 2013) has shown that evening primroses (Oenothera biennis) attacked early in the season by the Japanese beetle, Popillia japnonica, become more resistant to attack from seed predators than those that escape early season defoliation. As a result the beetle attacked plants produce more seed than those that escaped attack.  Given that a general measure of fitness is reproductive success (i.e. how many seeds are produced) then in this case, consumers do maximise plant fitness and Denis Owen can have the last word.

References

Belsky, A.J. (1986) Does herbivory benefit plants? A review of the evidence. American Naturalist 127, 870-892

Belsky, A.J. (1987) The effects of grazing: confounding of ecosystem, community and organism scales. American Naturalist, 129, 777-783.

Belsky, A.J., Carson, W.P., Jensen, C.L. & Fox, G.A, (1993) Overcompensation by plants – herbivore optimization or red herring. Evolutionary Ecology, 7, 109-121.

Choudhury, D. (1984) Aphids and plant fitness – a test of Owen and Wiegert’s hypothesis. Oikos, 43, 401-402.

Choudhury, D. (1985) Aphid honeydew – a re-appraisal of Owen and Wiegert’s hypothesis. Oikos, 45, 287-289.

Leather, S.R. (1988) Consumers and plant fitness: coevolution or competition ? Oikos, 53, 285-288.

Leather, S.R. (2000) Herbivory, phenology, morphology and the expression of sex in trees: who is in the driver’s seat? Oikos, 90, 194-196.

McArt, S.H., Halitschke, R., Salminen, J.P. & Thaler, J.S. (2013)  Leaf herbivory increases plant fitness via induced resistance to seed predators.  Ecology, 94, 966-975.

McLean, I., Carter, N., & Watt, A. (1977) Pests out of Control. New Scientist, 76, 74-75.

Owen, D.F. (1977) Are aphids really plant pests? New Scientist, 76, 76-77.

Owen, D. F. (1980). How plants may benefit from the animals that eat them. Oikos 35: 230-235.

Owen, D.F. & Wiegert, R.G. (1976) Do consumers maximise plant fitness? Oikos, 27, 488-492

Owen, D.F. & Wiegert, R.G. (1982) Beating the walnut tree: more on grass/grazer mutualism. Oikos, 39, 115-116.

Owen, D.F. & Wiegert, R.G. (1982) Grasses and grazers: is there a mutualism ? Oikos, 38, 258-259.

Owen, D.F. & Wiegert, R.G. (1984) Aphids and plant fitness. Oikos, 43, 403.

Owen, D.F. & Wiegert, R.G. (1987). Leaf eating as mutualism. In Insect Outbreaks (ed. by P. Barbosa & J.C. Schultz), pp. 81-95. Academic Press, New York.

Petelle, M. (1980) Aphids and melezitose: a test of Owen’s 1978 hypothesis. Oikos, 35, 127-128.

 

Post script

Denis Owen died at a relatively young age and for those interested in his career and life, his obituary can be found here.

 

 

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Re-examining external examining and the evolution of humans

External examining 2

Last year I wrote about my first year of being external examiner for the BSc Zoology degree at University College Dublin and some of the reasons why I enjoy the process.  This year I again visited Dublin to undertake my annual review of the zoology degree and was reminded of another reason why I find being an external examiner so rewarding.

Normally I go through all the exam scripts looking at how well they are annotated by the first marker, if they are signposted to help the second marker, e.g. marked as outside reading (OR) and check if they have been moderated and if the mark given has been justified in accordance with the marking criteria.  I also check if the marking across and between modules is consistent and fair.  For many of the modules this is really all I can do as I may not know a great deal about the subject, e.g. epithelial transport.  On the other hand there are some modules that I know a lot about, such as insect-plant interactions or biodiversity, where the questions asked are often very similar to the ones that I set for my own students. In these cases I read each answer and mark them before looking at what the actual mark given was and if they are similar this gives me confidence that all is well.

I often find myself learning new things when I read through the research projects of the students that I am going to viva; this year ranging from molecular biology, to phylogenetics, to elucidating the genes associated with inflammation of the brain of Irish greyhounds, to vertebrate behaviour to marine invertebrates and of course not forgetting entomology.  In respect to the projects this year the experience was no different.  What was different this year was that I had enough time to become engrossed with the scripts of the Evolution of Humans module.  One of the questions asked students to review the evidence that supports or refutes the theory that bipedalism in humans arose from adopting wading behaviour in a humid woodland environment. As a teenager, heretical as it may seem to my fellow entomologists, I was very interested in human evolution, reading and being influenced by Robert Ardrey, especially his book African Genesis and of course by the work of the Leakeys.  On reaching university and afterwards however, I became much more focused on invertebrates and my reading on human evolution became somewhat limited, although I do remember being unconvinced, rightly it seems, by the Aquatic Ape Hypothesis and sticking with the African savannah origin hypothesis.

I was thus fascinated to read about The Amphibian Generalist Theory (Niemitz, 2002) in which Carsten Niemitz put forward the idea that our hominid ancestors lived in trees in forested habitats as had been suggested earlier (Clarke & Tobias, 1995) but moved from there to forage along the nearby coasts and river banks from which they waded into the water in pursuit of the rich food sources available. The buoyancy given by the water and the need to keep their heads above water helped develop bipedalism.

Wading monkeys

Modern wading quadruped primates adopting bipedal locomotion whilst wading.  ‘Borrowed’ from Niemitz (2010).

Gorilla wading

Looks more like what happens when you get into water that is colder than you expect than foraging for food!

At the same time as the forests were fragmenting, the savannahs were forming and these were also able to be exploited by these early hominids. I found the student essays fascinating and they stimulated me to download lots of the papers that they referred to in their exam answers.  So as a direct result of external examining I have updated my knowledge of human evolution, and rekindled my interest in the subject.

This is, I think, a salutary message to us all, that by becoming too engrossed in our own subjects we run the risk of losing an all-round appreciation of the world in general.  Talking and listening to people from other disciplines is very important and can lead to very productive and exciting collaborations.  As an example, our entomology group at Harper Adams have  begun to develop some collaborative work with a psychologist, Claudia Uller, from Kingston University which will hopefully generate some very exciting projects.

And my final take-home message; if you are offered the chance to become an external examiner, jump at the opportunity and and not just auditing the process, take the time to read the essays and projects that are not directly in your area of expertise.  You will be pleasantly surprised.

References

Clarke, R.J., and Tobias, P.V. (1995) Sterkfontein member 2 footbones of the oldest South African hominid. Science 269:521–524

Niemitz, C. (2002) A theory on the habitual orthograde human bipedalism—the “Amphibische Generalistentheorie”. Anthropologischer Anzeiger, 60:3–66

Niemitz, C. (2010) The evolution of the upright posture and gaita review and a new synthesis.  Naturwissenschaften, 97:241–263

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