Perspectives Archives - Page 15 of 24

14/02/201409/02/2014

A review of the ecology of the common zombie

Abstract

In recent years fear of the zombie apocalypse has been an increasingly important subject in public media. Cinema, television, novels, both graphic and written, as well as computer games cover this subject more and more frequently. Public awareness of zombies has reached an historic height. However, within the scientific community this topic has rarely been investigated at all. The aim of this review is to summarise present day knowledge on zombies and assess its suitability in a possible encounter.

Generally, there is not much consensus regarding the nature of the common zombie, however a few traits seem to be found throughout the literature. Most sources agree that the zombie is a degenerate form of humans, lacking any form of higher intelligence. Some sources even describe them as devoid of any form of bodily function, defining them as the living dead. This would indicate that zombies have developed a unique way to transport carbohydrates, oxygen and carbon dioxide transport. One hypothesis is, that zombies are capable of consuming their own body for energy production. This is supported by the fact, that most sources describe them as slowly degenerating. Their main diet seems to be human flesh with a special preference for brain tissue. Most sources agree that the common zombie is indeed monophagous, refusing any other food source. Having effectively no brain function the zombie’s hunting strategy is limited to cursorial hunting. However, unlike more elaborate hunters such as wolves, zombies do not seem to display any cooperative strategies, even though the presence of human prey seems to trigger clustering of zombies. Even though most sources are agree that zombies have no natural enemy they have developed a remarkable defence mechanism. They can suffer significant amounts of injury, including destruction of the heart or complete blood loss, and still be fully functional. The only commonly accepted weakness of the zombie seems to be the brain, as severe brain damage is generally described to be lethal.

Generally it is accepted that zombies reproduce via infection, mostly through bites or when zombie blood gets in touch with an open wound. All sources agree that the human epidermis cannot be penetrated by zombie blood or saliva. Zombies are always described as r-strategists, showing rapid reproduction rates and no ability to adapt to changing environments, though some sources report the ability of zombies to hibernate for months or longer if no food is available.

We conclude that the zombie is a dangerous hunter which compensates limited rational abilities with an extreme endurance and low vulnerability. Their high reproduction rates makes them an extreme danger for any human society. However, due to their limited food range and lack of adaption to changing environments it might be possible to starve them out as any kind of muscle movement requires energy in the form of carbohydrates. Given their limited cerebral capacity it should be possible to effectively avoid zombies and therefore remove their only food source. Due to their high reproduction rate the population should collapse quickly even if single human individuals cannot avoid predation.

Author: Jesko Zimmerman, zimmerjr[at]tcd.ie

Image Source: Wikimedia commons

10/02/201405/02/2014

The Heat and Light of Science Communication

The recent debate between Bill Nye, the Science Guy and Ken Ham, the Young Earth Creationist got me thinking about our methods of science communication such was the controversy it generated.

There is value in communicating science to the lay public when our society is so deeply ramified by its discoveries, its ideas and its risks. And sometimes it’s easy to do so. For instance, there are people who find certain areas of research fascinating but may not have the expertise or money to read journal articles. This ‘gee whiz ‘cohort is actively interested in learning about the next big thing and will devour blogs, popular articles and newspaper reports. It helps to avoid a condescending tone (like saying gee whiz) if you have an inclination to write an article to this audience. As Steven Pinker’s editor put it “You should assume your readers are as smart as you are, as curious as you are, but they don’t know what you know and you’re there to tell them what they don’t know.”

This sounds very like the deficit model of communication, which states that, the only barrier to public understanding and skepticism of science is their ignorance. Provide the information and this deficit will disappear. I think this probably works for most of the non-controversial areas of science when the target audience is interested. I’m thinking of myself learning about subjects in physics or geology that are explained by the legion of science communicators that inhabit every form of multimedia today.

But we have a multitude of issues where the science is not accepted by a significant number outside the scientific sphere, notably climate change and the efficacy of vaccines. This is very problematic because the impact of these controversies threatens everyone, expert and lay person alike. How best to engage with these ‘deniers’? I’d argue that the problem here is fundamentalism. And how do you change the mind of a fundamentalist? To paraphrase Eugenie Scott, some people find the idea that they’re related to animals abhorrent and all the evidence supporting this isn’t going to change their minds. In other words, you don’t. The best we can hope for is that most of us are reasonable people and the lunatic element is just being especially loud.

When it comes to the evolution-creationism debate, many profs advocate the silent treatment; their rationale is that by engaging in debate we somehow elevate the status of the deniers. Much better, they say, to keep on churning out the books and interviews where there’s no risk of some rhetorician running rings around your PowerPoint presentation. Richard Dawkins and Stephen Jay Gould both shared this sentiment. With Dawkins arguing we should deny them “the oxygen of respectability in the world of real science.” But Dawkins has spent half a lifetime engaging with Creationists on different forums, on TV, in his books, and latterly on Twitter. I don’t see much difference. And surely scientists can muster up an individual who can speak sense to an audience while holding their attention with a stentorian voice.

So what about those people who are not particularly interested in scientific discovery but are concerned about the impact that certain fields of research will have on them? Or those of us who do not take the time to read about the controversy and may be swayed by entities like anti-vax campaigns? We have to have an included middle.

Unfortunately to some, certain theories can become “evidence-resistant” and that: “… as climate scientists know all too well, simply relating the facts of science isn’t enough. No matter that the overwhelming weight of evidence shows that climate change is real, or that vaccines don’t cause autism. When scientists find themselves just one more voice in a sea of ‘‘opinions’’ about a complex scientific issue, misinformation takes on a life of its own.” (Jackson et al. 2005)

One way to prevent this is to create a space for scientists to engage with the public, where they can engage in a dialogue. This is in contrast to the one-way, hierarchical approach of the deficit model I spoke of earlier. Jackson, et al.(2005) point out that when the public are left out of any such dialogue it should come as no surprise that they are distrustful of the outcomes of the resulting applications. The arrival of genetically modified organisms (GMO) demonstrated what can happen when there is a lack of upstream public engagement regarding contested science. Frankenstein Food campaigns should come to mind!

It’s also vital to frame science so that it’s easily accessible to the widest range of people all with different biases, beliefs, and ideologies. The anti-vax campaign is successful because it is framed with ‘Think of the children!’ the climate change deniers point to uncertainty of prediction; this coupled with the difficulty in conveying the danger of something that will take decades to manifest helps their campaign tremendously.

Another idea is to teach how science works to people at an early age. This is advocated by Arons who writing in 1983 comes at the issue of science literacy from a paedagogical standpoint. He says that scientific literacy is in a “lamentable state” and crticises the idea that it could be achieved through “verbal inculcation”. According to the author this approach seems to be little more than rote learning.The central point of Arons is his repetition of the idea that scientifically literate individuals should be able to answer “”How do we know …?” and “Why do we believe …?” questions”. If the majority of people were able to give an answer to these questions on the controversies mentioned here I think we’d have much less to lament about.

One trend to be picked out of the evolution of science communication is the realization the public isn’t monolithic either. And to clump every non-scientist into one social unit is a simplification too far. With ancient rhetoric and 21st century technology we have the ability to frame our arguments to every audience who will listen, reflecting their interests, fears and concerns.

References

Arons, A.B. (1983). Achieving Wider Scientific Literacy. Daedalus. 112 (2), p. 91-122.

Jackson, R Barbagallo, F Haste, H. (2005). Strengths of Public Dialogue on Science-related Issues. Critical Review of International Social and Political Philosophy. 8 (3), p. 349–358.

Author: Adam Kane, kanead[at]tcd.ie, @P1zPalu

Image Source: davidakirby.com

07/02/201422/01/2014

Please consider this a polite spanking

The recent hilarious #SixWordPeerReview hashtag on Twitter got me thinking about the first ever review I got for my first ever paper (thanks @Phalaropus for the reminder!). I thought I’d share it here (and if you want to see if you agree with the reviewer, the paper was eventually published in Global Ecology and Biogeography: Cooper et al 2008).

As a bit of background, I collected lots of data during my Masters project on life history traits of amphibians and then looked at macroecological correlates of clutch size, body size and geographical range size, and also at how these variables correlated with IUCN Red List status. My dataset contained over 600 species of amphibian – pretty much all the species I could get hold of data for at that time. Here are the “best” comments from the reviewer (the whole review was two pages long so I’m not reproducing the whole thing). My favourite comment was at the end.

“the study was done on less than 10% of the appropriate species […] Such academic laziness is inexcusable and scandalous”

“there are many instances where the authors appear to pull the wool over the reader’s eyes”

“It is a strong reflection of the workers to submit such a poorly conceived and obvious “quick and dirty” first stab at something that needs to be taken much more seriously”

“the clear misinformation in the abstract […] is obviously the kind of positive spin more associated with politics than science.”

“Who would be fooled by such tricks as claiming that data on <10% of amphibians is “large”. Certainly not this reviewer.”

“Without even a cursory explanation for such an egregiously low sampled diversity, it is hard to glean any merit at all from this study.”

“How can sane scientists think that <10% of the diversity would be sufficient to advocate involved analyses and draw conclusions?”

“This is another example of embarrassingly obvious laziness.”

“That goes beyond even forgivable bending of the truth”

“If any of the authors were thinking, they would have realized that ALL of the reasons to do a phylogenetically corrected analysis are not met by their data. In fact, if there was ever a gross and more ill-conceived reason to NOT do a phylogenetically corrected analysis, this would be the dataset to do so on.”

“Errors in basic addition are another serious embarrassment” [FYI the maths was fine, the reviewer made the error not us!]

“I could go on, but I think that it is not worth my time at this point to find more problems (there are still many other issues the authors should go back to first principles on)”

[And finally the crowning glory of all the comments I’ve ever received in a review]:

“Please consider this a polite spanking.”

As a first year PhD student this obviously upset me. But after a quick cry, a slice of Battenberg [cake], and a couple of pints of cider I was able to see the funny side! I still keep a print out in my office as a reminder that even when I get a bad review, it can never be as terrible as my first review! I’ve never worked out who the reviewer was, but as the editor said they were clearly having a bad day! I hope things got better for them! This review also reminds me to always write constructive comments, especially for PhD students, and if I don’t have anything nice to say I write a short review rather than airing all my grievances in print!

Author: Natalie Cooper, ncooper[at]tcd.ie, @nhcooper123

03/02/201421/01/2014

Levels of Selection

Thanks to the magical (and sometimes frustrating!) technological capabilities of Google+, every fortnight we have international phylo/macro journal club meetings which span three continents and even include elements of time travel (the Australian participants are always in the future!). Among the varied topics we cover, one of our recent sessions was a discussion of Samir Okasha’s book, Evolution and Levels of Selection. Evolutionary biology is an empirical science which also receives attention from philosophers. The two approaches are often difficult to reconcile so Okasha’s book is a welcome bridge for the gap between philosophical theory and practical biology. We mainly focused on the chapter which deals with species selection, clade selection and macroevolution and addresses the units of selection debate.

As a brief background, the debate hinges on the unit(s) and level(s) at which evolution by natural selection operates. Biological structures are inherently hierarchical. As researchers we tend to focus on specific organisational levels, so community ecologists will have very different concerns and interests to cell biochemists. Biological structures are shaped by evolution but the question is at which level(s) in the biological hierarchy does natural selection act? The theory of natural selection is an abstract concept; as Lewontin describes, the tripartite conditions for evolution to occur are phenotypic variation, differential fitness and heritability. So which level of biological organisation satisfies these requirements? Well it seems like it depends on who you read and who influenced your evolution teachers!

In the UK and Ireland we are generally taught evolution from a gene-centric point of view – the Dawkins school of thinking in which selection acts at the level of the individual and the unit of selection is the gene, and only the gene. However, across the pond, there seem to be more proponents and acceptors of higher or multi-level selection theory; the idea (following Stanley, Gould and Eldredge among others) that natural selection is not restricted to genes as the sole units of selection. It’s a confusing debate, especially when it comes to teasing apart the concepts of levels and units of selection; Okasha argues that a gene’s-eye view (genes as the units) can still be adopted for selection acting at various hierarchical levels. Furthermore, concepts of species level selection tend to become confused with group selection – a notoriously controversial concept which is guaranteed to set alarm bells ringing for many people.

Returning to Lewontin’s criteria, the basic idea of species level selection is simple. If species vary in some sort of traits and that variation gives rise to differential extinction or speciation rates, then some types of species will become more common than others. This approach is particularly common from palaeontological or macroevolutionary perspectives. If you’re interested in long-term evolutionary trends such as patterns of differential lineage abundances or extinction and speciation trends, it’s intuitive to treat the species as the level at which selection acts. This highlights a fundamental component of this debate: the gene-only-level of selection is usually advocated by microevolutionists; those who are interested in changes at the genetic level. In contrast, multilevel selection theory receives support from macroevolutionists who, due to their fundamentally different approaches, consider individual species to be their smallest units of interest.

When you think about species selection it is often easy to confound it with clade selection yet Okasha draws a clear distinction between the two concepts. Clades are, by definition, monophyletic; comprised of a single ancestral species and all of its descendant species. Unlike species, clades cannot split to create new clades with ancestor-descendant relationships because any new clade will inevitably be nested within the old clade (the diagram in Okasha’s book makes all of this far clearer than my description!)

Clade A is part of the larger clade B but it is not the offspring of clade B (offspring must have an independent existence from their parents and be able to outlive them).

Speciation and extinction rates are clearly not uniform; some lineages radiate into many different types of species which enjoy happy evolutionary lives (think of our arthropod-dominated world) while other evolutionary lineages produce fewer species. The question is whether these patterns are the result of species-level, macroevolutionary processes or whether emergent, species-level properties can be explained from selection acting at the genetic level. As an “acid test” for genuine species selection, Okasha proposes Elizabeth Vrba’s view that species selection must in principle (though not necessarily in practice) “be able to oppose selection at lower hierarchical levels”. Otherwise species level selection merely describes processes which can also be explained from a genetic-selection stance. For example, species selection may have been involved in the evolution or maintenance of sexual reproduction; the advantages of sexuality at the species level may have outweighed the two-fold cost of sex at the individual level and therefore favour the evolution of sexual over asexual lineages.

However, there seems to be a general paucity of clear examples which conform to Vrba’s acid test. One intriguing suggestion as to why this may be the case is time. The generation times of species producing new lineages are clearly far longer than the generation times of individuals’ reproduction so perhaps comparatively sluggish species selection processes have not had sufficient time to oppose evolutionary patterns which arise from individual selection?

Confused? It’s an interesting debate but certainly not one for the faint hearted and the fact that each philosopher/scientist/punter on the street seems to have jargon and slightly differing definitions of their own only serves to cloud the murky waters further. It is, however, interesting to contemplate how our own research backgrounds and the inclinations of our teachers influence our approach to the debate. If you’re interested in these kinds of questions then Okasha’s book is well worth the read or else you could join in with our Phylo/Macro journal club meeting; wherever you are in the world we’re on a Google+ hang out near you!

Authors: Thomas Guillerme (guillert[at]tcd.ie, @TGuillerme) and Sive Finlay (sfinlay[at]tcd.ie, @SiveFinlay)

Image Source: Okasha 2006, Evolution and the Levels of Selection

31/01/201421/01/2014

NERD club transferrable skills: reviewers, rejections and responses

Academic publishing: the currency of any research career. It’s all very straightforward; take your most recent ground-breaking results, wrap them up into a neat paper, choose the perfect journal, allow said paper to persuade an editor and reviewers of your brilliance and bask in the reflective glow of getting your research out into the world. Whether you see this rosy scenario as a target or delusional and unattainable aspirations, things rarely work out so smoothly. Instead, every researcher must learn to deal with the topic of one of our recent NERD club discussions; reviewers, rejections and responses. As a collective of staff, postdocs and postgraduate students, here are our thoughts on the dos and don’ts of dealing with the three r’s of academia.

1) Reviewers

Some journals invite authors to suggest reviewers or editors for their papers. If this happens, pick who you think is the “best” person whether that’s because the person is an expert in your field (although see our final point below), likely to give a fair review or because they are familiar with your work. Only suggest people to be reviewers if they have published themselves i.e. aim at the level of senior graduate student or from post-doc upwards. It’s also a good idea to choose someone that you’ve cited a lot in your manuscript (no harm to get on their good side). Equally, if you gave a conference talk recently, remember that person who seemed so interested in and enthusiastic about your work in the pub afterwards – chances are that they might be a fair and favourable reviewer. We also thought that, if you feel it’s necessary and you have a good reason, it might be a good idea to make an editor aware of people who you would prefer not to review your paper. However, be warned of the rumours that some editors may prefer to ignore such preferences and deliberately choose people from that “exclusion” list as reviewers.

In contrast, when selecting potential reviewers or editors, don’t choose someone who you have thanked in the acknowledgements of your manuscript. These are usually people who helped out or offered advice at some stage during the research so they would have a conflict of interest when it comes to reviewing the manuscript. Of course, you can also use this guideline to your advantage by seeking advice from and therefore acknowledging people who you definitely want to avoid as potential reviewers… Also from a conflict of interest point of view, don’t suggest your main collaborators, close friends or people from your own institution as potential reviewers. Similarly, for obvious reasons, don’t choose someone as a potential reviewer if you know that they dislike you or your work!

Once you have considered all these points, our final piece of advice about choosing reviewers or editors is don’t get hung up on it! Your preferred reviewers may not accept the manuscript, particularly if they are the senior, time-limited experts in your field. Finding reviewers for a manuscript is ultimately a lottery so, having thought about a few of our suggested guidelines, there’s no point in agonising over the process too much.

2) Rejection

It’s never pleasant to think about but your chances of rejection in all aspects of academia are high. Rejection of a manuscript can be particularly disheartening as it represents a dismissal of months if not years of your hard work. Our main piece of advice is not to do anything hasty. However unfair, pedantic or ridiculous the reasons which “justify” the rejection may initially seem, their bitter sting usually mellows if you take the time to sleep on it (after getting cross and having some comfort food/drink/other activities…). Similarly, don’t ruin your Friday evening/weekend/holiday by obsessively checking your emails for an editor’s response which will more likely than not be negative.

After hopefully returning to a somewhat more rational state, try to take the reviewer’s comments on board. The constructive ones will help you to make a better paper and parts which reviewers didn’t understand are often because you could have clarified your points better. Ultimately, it’s important to be realistic; the chances of rejection of a manuscript are high so be prepared to resubmit elsewhere (think back to our previous advice about working down the list of journals for which you feel your paper is suited). You could even have another version of the paper drafted and formatted for the next journal on your list even before you receive a response from your initial submission. It may take an initial investment in time and energy but at least the next version of the paper is then ready to go if you’re unlucky enough to receive a rejection from your first journal of choice. The most important advice to emerge from our discussion was to be thick skinned and not to take rejection personally. You can’t publish without experiencing rejection so it’s important to share your experiences (both good and bad) and to listen to the advice and woes others. You’re not alone!

Our final cautionary point was that you don’t necessarily have to accept rejection. If your paper was rejected on the basis of reviews which you think were poor, biased, unfair or just completely off the mark, it might be worth arguing your case with the editor and/or reviewers. HOWEVER, only take up this tactic in exceptional circumstances where you have a VERY strong case to back up your points. If you get a reputation for being petulant, argumentative, obstinate or just downright rude it can only serve to seriously aggravate an editor and damage your future publishing prospects if not your wider research reputation.

3) Responding to comments

Hooray! You’ve got through the reviewing gauntlet, dodged the cold blow of outright rejection and now there are just a few reviewers’ comments standing between you and potential publication glory. We came up with lots of dos and don’ts for how to deal with reviewers’ comments.

Most importantly, be polite and positive. No one was obliged to review your work so thank the reviewers for their comments and suggestions and consider adding them into the paper’s acknowledgements. Never be aggressive or rude and only write responses which you would be happy to say to a reviewer or editor face to face. Respond to all comments, no matter how trivial they may seem and show that you’re willing to make more changes if necessary. Don’t just ignore the bits that you don’t agree with. Show the editor that you have dealt with every comment by cross referencing the changes you made to the manuscript. To do this, either refer to the revised line numbers or, more preferably, cut and paste the sections that you have modified into your responses so that the editor doesn’t have to keep moving among different pages to check what has been changed.

Being polite and positive doesn’t mean that you have to be a push-over. If you receive a comment which is impractical, beyond the scope of your paper or just downright wrong, argue your point (with legitimate back up) but always retain a courteous tone throughout. If you have to deal with a whole slew of comments which are particularly off the wall or aggravating, ask someone to read your response before sending them to the editor – it’s always easier for someone else to pick up a passive aggressive tone which, despite your best efforts, may have crept into your writing.

If reviewers disagree on a particular point, either justify the changes you have made (don’t just ignore one reviewer’s comment) or your reasons for not making any changes. Don’t feel obliged to do everything that a reviewer suggests. Don’t ruin the flow of your text with awkward sentences which were clearly just inserted to please a particular reviewer. If you have good reasons (not just stubbornness or obstinacy) for sticking to your original ideas then make them clear. Remember that you can always get in touch with the editor if you get unrealistic or conflicting instructions or if you’re unclear about what you are expected to change.

So there’s our collective field guide to the trials and tribulations of academia. They’re by no means exhaustive but they’re definitely a good starting point. However, as academic publishing seems to require good fortune and timing as much as scientific rigour, research merit and an eye for a good story, there’s no magic formula for how to succeed, no matter how carefully you follow NERD club’s collective wisdom…

Happy publishing!

Author: Sive Finlay, sfinlay[at]tcd.ie, @SiveFinlay

Image Source: justinholman.com

24/01/201410/01/2014

Science and Journalism

As scientists with access to hundreds of peer reviewed journals its easy to forget that we are a privileged bunch. We get to read science straight from the horse’s mouth without anyone to get between us and the research. Yet for the majority of people journals are hidden behind paywalls and even open access journals remain largely the domain of working scientists if for no other reason than reading scientific journal articles is hard work. They demand a high level of prior knowledge and often use terms that are completely meaningless to anyone outside their field. It’s no surprise that the majority of people get their science news from newspapers.

The problem with science in newspapers is that it’s really badly done. It’s often based on press releases from universities and others have written about how the media will take a story and run in whatever direction they please, regardless of the actual research. Science journalism has been relegated to the side-lines. While it would cause outrage if someone who knew nothing about football was allowed to write in the sports section, non-science journalists are regularly writing science stories, unable to critique the work or put it in any context. On the one hand it leads to sensationalist stories but on the other it can result in the real news story being buried among trivialities (something I’ve written about before).

It’s one thing to disagree with a news story about your own research but what about other science stories? If you have any interest in science chances are you’ve read a news story and shook your head in disbelief at the poor reporting. You may have moaned about it to friends until they wondered off saying something about “letting it go” or “getting a life”. But what, really, can you do? You’re just one person. . .

Well, it turns out there is something you can do. You can email the journalist. You can explain, politely and calmly, exactly what was wrong and then suggesting ways of making the story better. So, rather than say;

“Your article was rubbish, you don’t have any idea what you’re on about it was all wrong!”

you could write,

“I was disappointed by your article. You said that whales are a fish when they are actually mammals”.

(Hopefully you won’t see any errors that egregious!)

You may be thinking that it’s all very well and good to email them, but why should they listen? Why do they care? The story’s finished, they’ve moved on. Well, one reason is that most stories are online where they form a permanent record, so any errors will remain forever unless corrected which does nothing to help a journalist’s reputation. Secondly, most of the errors aren’t out of spite or even callous disregard, it’s because they don’t know any better. As I said, a lot of science journalists aren’t experts so they’re going to make mistakes. Even if do have a background in science they can’t know everything. Could you write as well on quantum mechanics as you could on evolution, for example? I doubt it.

This all sounds wonderful. You see an error in a science story, you email the journalist and he corrects it and everyone goes merrily on their way. Really? Life isn’t that pleasant. Well, actually, it can be. The inspiration for this post came from an article I saw hyperbolically titled “New species of terrifying looking ‘skeleton shrimp’ discovered”. The original article gave no information about who had discovered the animal or why it was important. It also had incorrect formatting on the genus and family names. I emailed the author and politely explained the problems. I had a lovely response and he corrected the formatting errors, added the information it lacks and, most importantly, gave credit for the discovery where it was due. The article now online is the amended one and while still not brilliant, is much better.

The moral of this story is that if you see bad science in the news contact the journalist. Chances are they don’t know they’re making mistakes and as long as you are polite and specific they will heed your advice. While you won’t get a 100% success rate, or even a 100% response rate, you will get some response. Focus on the smaller articles usually written by people low down the hierarchical food chain who are most receptive, who haven’t been jaded and welcome polite, constructive advice and can be encouraged to do better in the future. If we all make the effort to correct bad science reporting we can hopefully help journalists and improve science understanding in the public domain. Not bad for one email.

Author: Sarah Hearne, hearnes[at]tcd.ie, @SarahVHearne

Image Source: blogs.discovermagazine.com

20/01/201414/01/2014

NERD club transferrable skills: academic authorship and journal submissions

We rolled out of bed on January 6^th, 2014, with the somewhat comforting- but mostly jarring, give-me-a-cup-of-coffee-immediately-inducing- knowledge that the holiday season was over and it was time to get back to our normal schedules. And that happily means everyone once again gathers for Nerd Club before lunch on Tuesdays. Aided by left over boxes of Roses, the first Nerd Club meeting of 2014 kicked off with a transferrable skills session discussing the submission of papers and how to cope with the peer review process. Many of the PhD students in the group (myself included) are working towards our first, first author paper. It can be a long and discouraging process, so we were eager for advice from our more experienced members.

We wanted to cover four topics; (1) issues of authorship, (2), choosing a journal, (3) choosing and responding to reviewers, and (4) dealing with rejection (sniff!). I’m going to summarize our discussion on the first two points, which we talk about during week one of this two-week session.

Issues of authorship

Who should be included; criteria for authorship

We came up with several ways to determine exactly who should be included as an author on a scientific publication. A popular method is asking, “could this paper have been completed without his/her contribution?” A common issue with this method is considering technical support. A research assistant or undergrad for example may spend hours helping with an experiment; perhaps without them you wouldn’t have completed the work. If there was no intellectual contribution however, some argued there may be grounds for excluding such a person as an author. A similar question one can ask is, “has the paper been made materially better by the person?” Again, you run into the same problem; what about editors, and how much exactly does someone need to contribute to qualify? One extreme view is that you should refuse authorship on a paper unless you feel you could give a talk about it. While this is a great goal to aspire too, there was some controversy in the room on the feasibility; what if you did a substantial amount of modeling for a paper and without your contribution it would not have been published, but the paper was on an area in which you have little expertise? You may understand your contribution completely, but that doesn’t mean you’re ready to discuss Type I diabetes or the complexities of insect flight. In general the group agreed that you should at least be able to discuss the main goals and conclusions of the paper, even if you wouldn’t present it at a conference. More and more journals (Proceedings B, Science, etc.) are requiring a section listing each author’s contribution, so it’s a good idea to make these decisions early as you will be held accountable for them when you submit.

Another piece of advice that seems to fall under the “who” category is how to decide on the author affiliations listed on the publication. Usually the affiliations from where the person did the work are the ones that should be included, even if the person has moved on to another job or institution. It is possible, however, to add a current address so that authors can still be contacted by readers.

Two final piece of advice: first of all, if you’re the first author on a paper, it is probably your responsibility to start this discussion and to make final decisions on who will be included (of course for PhD students it’s going to be necessary to consult your supervisors). Second, if your name is listed as an author you should at some stage read the entire paper in detail and make helpful comments, not only to improve the quality, but also to ensure you understand the work and conclusions completely.

What are the most important names on the list?

I think most of us were aware that there are two important places in that sometimes-long list of authors, first and last. First author is the person driving the work, who usually claims the most ownership. The first author will get the most recognition for the paper among the scientific community as well. Some journals allow co-first authors, however someone’s name will have to be placed first on the list. When I read a paper, if there are more than two authors I almost always remember only the first, and I’m not alone.

The last author is considered the senior author, the person who likely received the funding to do the work and who probably leads the lab or research group the first author is working in. Surprisingly to some of us, it is possible in some journals to have co-senior authors as well.

Finally, the corresponding author is the person who will physically submit the paper and is responsible for responding to reviewer’s comments. They are also the one to contact if someone has a question about the work. Overall we decided that corresponding author singles one of the people on the list out, but it doesn’t really distinguish them in any other way.

When to discuss it and make changes?

The consensus from our group was that yes, issues of authorship can sometimes be awkward and complicated, but it is important to have conversations about it early and often with your collaborators. Otherwise a slightly uncomfortable situation can turn downright ugly, and can cause rifts between research groups and partners. So, to avoid discomfort, talk about authorship as soon as possible and throughout the writing process.

We also discussed adding and removing people from your author list. It is usually fine to add an author at almost any stage, so long as you feel their contribution was worth authorship. Removing an author at almost any stage is usually uncomfortable. Because of this, if you’re in a situation where you feel you did not contribute enough to a paper to be an author, it is best practice to ask to have yourself removed. If your coauthors refuse, then at least you can publish with a guilt-free conscious. Of course if at any stage you don’t agree with what is said in a publication or you feel something unethical or unscientific was done, you have the right to insist that your name be removed. Never publish anything you don’t believe in or agree with!

Where in the list your name appears; highlighting your research

A really useful piece of advice: if you find yourself in the middle of a long author list-but you know you’ve contributed in a significant way to a paper- don’t be afraid to star or highlight this on your CV. It’s really important to show future employers that you had a meaningful role in the process, and to highlight you skills.

Choosing a journal

After a rather lengthy discussion about authorship, we had a little time left to talk about how to choose a journal for your publications. We did come up with some helpful methods and tips. First, your paper must obviously fit the aims and scope of a journal. Second, you can choose a journal based on its readership- will your research get to the people you want or the people that will care about your work? We thought that in an age where people rarely if ever sit down with a physical journal or magazine, this isn’t always the best way to go (although perhaps you can choose by who you think will receive the table of contents in their email box!) Third, some choose by the impact factor of the journal, a perhaps less idealistic but more realistic view of the process. Yet another method is looking at where most of your citations came from, and trying to submit to that journal. And finally there are practical reasons to choose a journal such as word count or number of figures allowed.

There were two pieces of advice I found particularly helpful in this discussion. First, consider having a list of possible publications you would submit to, in the order you would attempt, before writing. It can be soul crushing to write a beautiful paper for Biology Letters, with its strict structure and word count, only to be rejected and required to completely rewrite a draft for a different journal. Perhaps you have the time to do this, but if it’s the final year of your PhD that may be a poor idea. Finally, when constructing said list, have the top 20 journals in your subject(s) printed out, and highlight the ones you tend to like to make the choices easier.

Stay tuned for the next installment of this series, where we will summarize our discussion on choosing and dealing with reviewers and dealing with rejection- a topic we’re all sure to face throughout our scientific careers.

Author: Erin Jo Tiedeken, tiedekee[at]tcd.ie, @EJTiedeken

Image Source: phdcomics

17/01/201417/01/2014

Killing in the Name of Science (Part 2): What About the Bunnies?

In my last post I wrote about the case for scientific whaling. I tried to be objective and leave moral and ethical considerations out of the discussion to focus solely on the science. Yet it is impossible to avoid these considerations for long. The use of animals in scientific research has a long history and has engendered debate for much of that time. Legislation to protect animals against being used in painful experiments was introduced back in the 19^th Century through the Cruelty to Animals Act which became law in 1876. Amendments have been made to provide greater detail on what and is not permissible, in Ireland most recently in 2002 and in the UK in 2013.

The ethics and utility of animal research is a massive and complex topic and one which I cannot hope to cover in a simple blogpost. It is also a highly contentious topic with advocates on both sides of the debate. Most of the controversy surrounds the use of animals for medical research and cosmetics testing which has been argued against by organisations such as the British Union for the Abolition of Vivisection (BUAV) and People for the Ethical Treatment of Animals (PETA). Looking at their websites you would quickly believe that all animal research was pointless and cruel. One statistic on the BUAV website is that only 13% of animals used in the UK are for medical research. This is true, but it’s only part of the story. UK government statistics from 2011, the most recent year with available figures, show that almost 3.8 million vertebrates were used in animal research, of which almost 43% were used in the breeding of genetically modified or harmful mutant animals and 35% were used in fundamental biological research. So while the impression being given by the BUAV is that 87% of animal experiments are a complete waste of time, the reality is a bit more complicated than that.

However, I don’t wish to use my time here to debate the use of animals in medical and cosmetics testing. I don’t have the expertise to discuss the rights and wrongs of medical testing and cosmetics testing is a largely moot point as it is banned in the EU. What I would like to discuss is the use of animals a wider context and examine why we care more about some animals than others.

The Cruelty to Animals Act specifically and exclusively protects vertebrates. The UK amended their version of the law in 2013 to extend this protection to cephalopods. Yet this Act and its companion, the Animal Welfare Act 2006 only cover vertebrates and also exclude certain activities, most notably fishing. (Apologies for referring to the UK versions of these laws, I was unable to find the Irish equivalents. The closest I could come to the Animal Welfare Act was the Animal Health and Welfare Bill which is still in draft form).

It is here that I want to start my discussion. Why are fish that are kept as pets or used in laboratories covered by law against being treated cruelly yet fish that are caught by a recreational angler or a commercial fisher not? According to the figures, 563,903 fish were used in scientific research in the UK in 2011. In the same year the UK caught 12,700t of cod or approximately 1.6 million fish. Just one fishery accounts for almost 3 times as many fish as were used in all of scientific research yet the law does not concern itself with their wellbeing. Why not?

The obvious reason is cost. Can you imagine the time and effort required to humanely euthanise every fish as it came on board? It would be completely unmanageable and would make fisheries impossible to be commercially viable. But it does raise the question of why we care about the fish in labs but not those on boats. They’re still vertebrates, a group we have deemed worthy of protection, yet when it comes to the choice between humane handling or cheap fish and chips we chose the latter with little difficulty. I’m not saying this is right or wrong, just that it is interesting.

Going back to my previous post, it would be hard to find someone who was indifferent to the suffering of the whales killed for their stomach contents. Yet my alternative option of killing thousands of krill would likely raise little or no reaction. Why are a thousand deaths preferable to one? This is even more puzzling when you consider that until recently whales were seen as little more than as a source of food, oil and baleen. They have gone from being the marine equivalent of cows to a creature people pay huge amounts of money to see.

These may seem like facetious questions unworthy of dignifying with a response. We protect whales because they are intelligent animals who clearly experience suffering. Krill, on the other hand, are effectively prawn crackers without the cracker and are undeserving of concern. But again I’d ask, why? Why is intelligence the marker we use for whether something is worthy of compassion? Why would we happily kill thousands of invertebrates to save the life of one vertebrate? And why are some vertebrates more worthy than others? Efforts have been made in recent years to make whaling more humane as we have come to appreciate whales for more than their commercial value yet there has been no attempt in other fisheries. Fish and squid still suffer agonisingly slow deaths on board fishing vessels around the world while their lab-based compatriots are given lives of luxury followed by an endless sleep induced through overdoses of anaesthesia.

It is human nature to value some things over others. We care more about our family than we do strangers on the other side of the planet. I suspect that this in-group favouritism extends to the animal kingdom which is why we care more about primates than mice, and more about mice than fish, and more about fish than snails. I also suspect there is an element of “appeals to cuteness”. Seeing a dog staring at you with big puppy-dog eyes pulls at the heartstrings in a way a snail can never achieve. Yet while it is understandable, I guess my final question is, is this justified? Should we really care more about cute mammals than ‘slimy fish’? Should our level of caring be contingent on the economic consequences of caring? All other things being equal, if research is worth doing does it matter if it’s done on a snail or on a mouse, and if it doesn’t should the snail be the animal used every time?

I don’t have answers to any of these questions. There may not be answers to these questions, or at least not objective answers. However, just because they may not be answerable does not mean the questions should not be asked. Animal research is a vital part of biology. Even if medical testing stopped tomorrow, animals would still be used in research laboratories for a host of legitimate and necessary reasons. It will likely always be a controversial subject and we owe it to ourselves and the animals to continue to question our assumptions, biases and justifications for our utilisation of animals in scientific research.

Author: Sara Hearne, hearnes[at]tcd.ie, @SarahVHearne

Image source: Wikicommons

13/01/201423/12/2013

A brave new world of monkeying around with trees

I’ve spent the last few days writing an introduction for my first PhD paper on the practical issues of adding fossils to molecular phylogenies (full recipe here). This is my starting point: most people working in macroevolution agree that we should integrate fossils into modern phylogenetic trees. Of the many possible methods that are available, Ronquist’s total evidence method looks to be the most promising (however, some nice other ones also exist).

Recently Schrago et al. published a nice attempt to use this method on the Plathyrrini (New-World monkeys to you and me):

As a reminder, the aim of this total evidence method is to combine all of the available data: both molecular and morphological. Traditionally, analyses have treated each type of data separately; approaches which bring their own advantages and problems.

Let’s start with the molecules:

Opazo et al. published in 2006 a classical example of a molecular phylogenetics study. There are more recent, impressive phylogenetic studies (like Perelman et al. in 2011 and Springer et al. in 2012) on most of the primates and using more genetic data but I think Opazo is a better example of a traditional approach because it involves a tree with 17 taxa instead of more than 200.

Opazo.et.al~2006-Fig5 — Opazo et al. 2006 Fig. 5. A Platyrrhini dated phylogeny – values indicate the age of the nodes, the circle at the root of the tree is the fossil used for age calibration: Branisella.

Two of the main advantages of this approach are the quantity of data involved (tens of thousands base pairs) and the methods of inferring the evolutionary history: molecular evolutionary models are easy to understand and easy to implement (each site has a finite number of states – A, C, G, T or nothing – and probabilistic models are good enough to infer the rate of changes from one state to the other). From a data perspective, another practical advantage is that, with modern NextGen sequencing, it’s really easy and fast to obtain a full genomic dataset. However, the main inconvenience from a macroevolutionary point of view is that molecular approaches don’t really take evidence from the fossil record into account. In the Opazo example, the only fossil used is Branisella, and the only useful information here is just its age (around 26 Ma) used to calibrate the time on the tree.

On the other hand, Kay et al. 2008 published an awesome study of the Platyrrhini history from a palaeontological point of view. They focused on 20 living taxa combined with 11 fossil species and using 268 morphological characters.

Kay.et.al~2008-Fig21 — Kay et al. 2008 Fig. 21. A Platyrrhini phylogeny based on morphological data including fossils.

Again, there are both advantages and problems associated with this approach. Firstly, the number of characters used is pretty low; don’t get me wrong, 268 is really good for a morphological matrix, it’s just low compared to molecular data. Furthermore, the underlying evolutionary models used to build the phylogeny are hard to infer, the most common model is the Lewis 2001 Mk model where morphological characters are treated as if they “act like” molecular sites with no assumptions made about their states or rates of change (this method has been criticized but it’s still our best way to infer morphological evolution). Another solution, which is also commonly used, is to infer nothing but instead just use a maximum parsimony approach: find the tree which explains observed phenotypic evolution with the fewest number of evolutionary steps (characters changing from one state to another on a particular node within the tree). However, compared to a purely molecular approach, the advantages of Kay’s tree are clear from a macroevolutionary point of view: this tree includes full information from the morphologies of both living and fossil species!

Now hopefully you can see where I’m coming from in wanting to use the total evidence method? It’s clear from the empirical examples above that the problems associated with one approach are the advantages in the other. So let’s just combine them! And that’s what Schrago did in their work, they just mixed both data sets and re-ran the analysis (or, more precisely, they used Kay’s data set as it was but added new genomic data collected over the last seven years to Opazo’s data set). Here’s their result:

Schrago.et.al~2006-Fig2 — Schrago et al. 2013 Fig 2. Phylogeny of extant and extinct Platyrrhini using both molecular and morphological data.

So here we have the advantage of both methods combined and this tree is far more user friendly for macroevolutionary studies; one can test evolutionary hypothesis through time using a more complete representation of the Platyrrhini evolutionary history. One major problem still remains though; the paucity of useful morphological data compared to the wealth of molecular data which is now available. Does that influence the tree’s topology somehow? Well, stay tuned, my simulations are running…

Author: Thomas Guillerme, guillert[at]tcd.ie, @TGuillerme

Photo credit: wikimedia commons

10/01/201407/01/2014

Killing in the Name of Science (Part 1): The Science of Scientific Whaling

“The research reported here involved lethal sampling of minke whales, which was based on a permit issued by the Japanese Government in terms of Article VIII of the International Convention for the Regulation of Whaling. Reasons for the scientific need for this sampling have been stated both by the Japanese Government and by the authors.”

With these words I realised I’d stumbled on that semi-mythical creature, a paper that was the result of scientific whaling. Scientific whaling, if you don’t know, is how the Japanese government justifies hunting whales. Whales have been hunted since time immemorial but due to advances in technology by the mid 20^th Century stocks were overexploited to such an extent that many species were pushed to commercial extinction (and possibly, such as in the case of the North Pacific right whale, actual extinction). In 1986 the unprecedented action was taken to ban commercial whaling globally to allow populations to recover. Since then small numbers of whales have continued to be caught, almost exclusively by counties with strong historical ties to whaling such as Norway, Iceland and Japan.

Whales can be caught either commercially or for science. Norway and Iceland whale commercially, selling whale products both locally and internationally through a carefully controlled trade. Japan catches whales for scientific purposes and then sells the meat in accordance with the rules of Article VIII of the Convention. According to the Ministry of Foreign Affairs of Japan,

“The research employs both lethal and non-lethal research methods and is carefully designed by scientists to study the whale populations and ecological roles of the species. We limit the sample to the lowest possible number, which will still allow the research to derive meaningful scientific results.”

The paper that caught my interest is titled “Decrease in stomach contents in the Antarctic minke whale (Balaenoptera bonaerensis) in the Southern Ocean”. There are several ethical questions that the paper raises:

1) Can the samples be obtained without killing the whales?

2) Was the sample limited to “the lowest possible number” that allowed “meaningful scientific results” to be obtained?

3) Was the science worth it?

The first question is arguably the easiest to answer. Investigations of stomach contents commonly requires killing the animal whose stomach contents are desired. While non-lethal methods are available, they are difficult, time-consuming and are most effective on small animals in a captive environment. Thus the killing of whales to examine their stomach contents is not unreasonable.

The second question is harder to answer. Over the course of the 20-year study period, 8,468 whales were killed by the Japanese, an average of 423 minke whales per year. Of those, 5,449 had stomachs containing food, or 279 per year. This sample size is definitely sufficient to give statistically significant results but is it ‘overkill’ (to use the obvious pun)? Looking through my collection of papers on diet analysis, it definitely appears so. A brief survey showed that sample numbers generally range in the low tens (10-50) of specimens. Numbers only went up when sampling commercial species (such as squid or fish) or when opportunities arose. If smaller numbers are accepted by the research community, questions must be asked as to why such high sample numbers were deemed necessary. Of course, if the whales were sampled for other studies and this study was simply an attempt to use the data in as many ways as possible then my concerns are baseless.

The final question is also the most contentious. Who is to say whether the science is worth it or not? The Ministry of Foreign Affairs of Japan said that its research:

“. . . is carefully designed by scientists to study the whale populations and ecological roles of the species. . . The research plan and its results are annually reviewed by the IWC Scientific Committee.”

If it has been assessed by the Japanese government and the IWC (International Whaling Commission) as being necessary, who are we to argue? We need to carefully look at the research being done. On the basis of this paper, I am not convinced. The study uses stomach content analysis to determine that krill availability (the food source of minke whales) has decreased over the last 20 years. Two hypotheses are put forward to explain this decrease: krill populations are being affected by climate change or there is increased interspecific competition for krill as other species increase in population size due to reduced hunting pressure. They conclude:

“Thus, continuous monitoring of food availability as indicated by stomach contents and of energy storage in the form of blubber thickness can contribute important information for the management and conservation under the mandates of both the IWC and CCAMLR of the krill fishery and of the predators that depend on krill for food in the Southern Ocean”

I disagree. They are using stomach contents as a proxy for assessing krill populations, yet it would be far easier and less ethically challenging (something I will return to in my next post) to simply sample the krill. I can see little reason why lethal sampling is required to collect this data, though I’m happy to be persuaded otherwise.

Having not been convinced by this study, I was still willing to believe that scientific whaling was producing good, robust, scientific data that could not be obtained through non-lethal methods. In my search for confirmation or rejection of this hypothesis I came across this report entitled “Scientific contribution from JARPA/JARPA II”. It lists publications that have resulted from Japan’s scientific whaling for the period 1996-2008. In that time, 101 peer-reviewed articles were published and 14,643 whales were killed, 88% of which were minke and 79% of those caught were caught in the Antarctic. Yet despite this seeming wealth of data, the IUCN still considers the Antarctic minke whale to be Data Deficient. Given that most of the papers that have been produced as a result of scientific whaling are related to stock assessment, the lack of an accepted stock level is rather telling in its absence. The rest of the papers seemed to be related to genetic studies, which are possible to do without lethal sampling.

This is, admittedly, a very preliminary survey of the literature resulting from scientific whaling. It can also be claimed that as an ecologist I’m against whaling regardless of the scientific or economic merits. This is not the case. As a disclaimer, I have eaten whale meat while in Norway. It is a sustainable fishery which is carefully monitored. In fact, if I was to feel morally dubious about anything from that meal it would have been my main course of halibut, which has been systematically overfished.

This raises other ethical questions which I hope to address in my next post. However, for now, a conclusion is due. And in my mind it is this: the science that is being produced through scientific whaling does not justify the number of whales being caught. Most of the science can be done through other sampling methods and that which cannot has not been shown to be necessary. Given the costs, the controversy and the decreased ability to sell the meat the case for scientific whaling rests on the quality of the science and ultimately that science is lacking.

Author: Sarah Hearne, hearnes[at]tcd.ie, @SarahVHearne

Image sources: Wiki Commons and Sarah Hearne