Archives: Biology

Bibbreviate: a Python package for BibTeX journal abbreviations

Journal abbreviations and BibTeX drive me nuts.  Some journals demand that you submit manuscripts with abbreviated journal titles in the bibliography, while others want fully spelled-out names.  The only solution that I’m aware of is to keep two .bib files, one with abbreviate names and one without.  However, this means keeping two .bib files up to date, and I don’t know how people do that without tearing their hair out.  This got so annoying that I finally wrote a Python script to use the JabRef abbreviations lists to flip back and forth as needed.  That way, I can keep one master .bib file and abbreviate it when I need to.

The results aren’t always perfect, but they do cut out 90+% of the find-and-replace work needed to handle a journal that asks for abbreviate titles.  If you need that too, you can download the package from pypi, or grab it from my GitHub repo.  Fixes and feature additions are welcome, so feel free to fork it and send a pull request!

Science isn’t a pizza, so stop slicing it up.

Science isn’t a pizza, so stop slicing it up.


Praj, author of the blog Do I Need Evolution, drives me nuts. Don’t get me wrong, he seems like a nice guy and a well-meaning one at that. Yet as one of the new wave of commentators on the science vs religion battles, he appears to hold a view that basic science is just an indulgence that we should be quiet about in favour of the real science that puts satellites in the air and cures diseases:

You see two images when scientists speak about “science” (something I think we should avoid, but that’s another story). One is science as a useful tool: it helps us cure diseases, win wars, grow the economy, feed the planet, and so on. The other is science as a world-view: it imparts a sense of wonder, conquers fear, and reveals beauty. These images are a spectrum rather than distinct categories. Most scientists have some of both, though applied researchers are usually closer to the science as a tool view and basic researchers tend to be on the other end.

The problem is that the overwhelming majority of non-scientists, and especially the religious, don’t care very much about science as a world-view. They live on the very far end of the spectrum where science has almost zero intrinsic value. To those people science only matters because it helps them do stuff they care about.

Science lobbies appreciate this fact, which is why they focus on the concrete, tangible benefits of research. They know it would be ridiculous to ask for billions of dollars because some people think particle physics is beautiful. Policy experts also appreciate this fact. The standard “explain your thesis to your grandmother” interview question for my DC fellowship is judged on how well you make your research relevant. I suspect many academic scientists don’t appreciate this fact. Or if they do, they don’t weigh it as much as they should. Academics are especially prone to hyperbole about the wonders of science.

Praj would like us to think of science as more or less practical; some science will give us economic benefits, and can be explained in that light, so that’s good. Other science is ‘world-view’ science that only exists to satisfy the whims of a subset of curious people. But I’m going to disagree here and say that Praj doesn’t understand science very well. Despite lip service to a ‘spectrum’, he would like to slice science up into boxes that can be addressed independently. That way, we can focus on ones that are practical, and ignore ones that aren’t 1. But we can’t do that with science. Science is a process and a body of knowledge that is interconnected and historically contingent.

As an example of interconnection, we can look to Darwin himself. Putting aside for the moment the historical antecedents to his work on evolution (including Lamarck and his own grandfather), Darwin had to integrate ideas from all corners of biology with the work of the economist Thomas Malthus to arrive at his insight regarding natural selection. In order for this theory to be sensible, it required a much older earth, ideas that came in part from the volumes of the geologist Charles Lyell that he read while on the Beagle. One of the first serious scientific challenges to evolution came from the physicist Lord Kelvin, who calculated both the age of the earth and the age of the sun before concluding that both were too young for evolution to be valid. This phenomenon has only gotten stronger over time. We carve fields like biology, physics, chemistry, psychology, etc. up into separate fields because we have to have a way to award degrees, and topics can indeed be thought of as clustering together naturally. Most ecologists don’t study quantum field theory, because with our current understanding of science, it’s hard to see how to use it effectively in their work. But that doesn’t mean that we can take those lines in a course catalog as representative of some real and sharp division. What we call biology and chemistry are deeply interrelated, as anyone who’s spent time in a molecular biology lab will tell you. Neuroscientists spend a lot of time on the biology and chemistry (and by extension, biophysics) of the brain and nervous system. One of my favourite evolutionary biologists is John Maynard Smith, who trained as an aeronautical engineer, and we all know that physicists are math fetishists (I kid, I kid). Just look at the new interdisciplinary fields that are cropping up with increasing frequency: biophysics, neurochemistry, behavioural and neuroeconomics, agrophysics, systems biology, computational sociology. And I could do this all day, because science is a heavily connected graph of fields that reflect an underlying continuum in our study of nature. Apparent divisions in scientific fields usually reflect more about our lack of understanding than they do of any real separation.

This brings me to my second point, the historical contingency. Praj and people like him would like to focus on ‘practical’ science that we can make relevant for the public. Things that bring economic benefits now. ‘Applied’ science, new technology, and so on. But people who champion this division between basic and applied research are making a simple mistake of perspective, one that even serious historians of science are prone to making. What is considered applied science now relies directly upon research that used to be considered basic and impractical2. Applied science is simply science for which the next step on path is to an economic benefit that is clear and predictable, but ‘practical’ or ‘applied’ science doesn’t get to walk away and ignore this chain of connections and history. Putting a satellite into orbit relies on centuries of work in physics and mathematics that was once considered deeply impractical. It is the result of thousands of individual steps, some practical, some not, that have given us the ability to put things into orbit. Medical doctors rely on work in anatomy, biochemistry, and biology that has often been considered very impractical (Galen himself wasn’t allowed to work on humans because work on cadavers wasn’t permitted; he inferred from animals because of their anatomical similarities). Astronomy and cosmology are the prototypical basic and useless sciences now, but if we ever become a truly space-facing people, then our descendants will be very happy that we wasted our time on it for the simple pursuit of knowledge. And who knows? Astronomy and cosmology could suddenly become very useful before that; we can’t easily predict what will be applicable, but the history of science tells us that we can expect to be surprised. I’m sure that the Einstein of 1945 would have had some words to say on the topic to the Einstein of 1905.

Praj would like us to believe these things about science, because he wants to believe that Bill Nye is wrong when he says that creationism threatens our ability to understand the world and innovate in science and technology:

I’ve often wondered how people like Bill Nye can maintain this apocalyptic vision. As Saletan notes in the very next paragraph, there are actual, real-life engineers and scientists who reject evolution.

Praj himself relates that his parents were successful doctors and his dad doesn’t understand evolution, so evolution must not be relevant to medicine. He make similar claims several times on his blog, so it’s worth finishing off this post by addressing it. Yes, there are successful doctors and engineers and even other scientists (though few if any biologists) who don’t understand evolution. That is, of course, not the same as saying that they actively reject it and believe in young-earth creationism. There’s a difference here. I don’t understand much about particle physics, but though I consider that a failing it’s one I can live with. There isn’t enough time in the day for me to learn everything I would like to. And yes, doctors who haven’t learned about evolution aren’t necessarily bad doctors. I can even forgive those who ‘reject’ it because they’ve never been exposed to it properly. But doctors who actively reject evolution when taught it, and believe that the earth is 6000 years old? This requires that they actively read and reject the evidence from not just biology but physics, chemistry, geology, and so on. This requires that their critical thinking skills are so deficient that they cannot understand and assimilate anything of such a large and coherent body of evidence upon which there is broad and solid scientific consensus. How can this be a good doctor or engineer? Would you like your satellite designer to be a flat-earther? Would you be worried if your bridge engineer was proficient but convinced that physics and material science works as it does because of the action of ambitious fairies?

When my doctor asked what I did for a living and then launched into a tirade because he was a young-earth creationist, I asked him how he dealt with giving advice to his patients on vaccination or antibiotics. He replied that he didn’t believe in vaccination and that he didn’t think that antibiotic resistance was a problem, because viruses and bacteria don’t evolve. I changed doctors that day. This is a man who may actually kill patients with advice like this, and it stems directly from his religious beliefs. Are all creationist doctors and engineers bad at their jobs? No, but I submit an empirical hypothesis that doctors, engineers, and scientists who are actively creationist (especially YEC) and reject scientific understanding to protect their beliefs are more likely, on average, to be bad at their job and to have crucial deficiencies in their thinking that could prove harmful to their work.

Science isn’t something that can be cleanly chopped up into convenient portions and picked over for economic benefit or religious palatability. It is a method, the best method we have, for discerning the truth about the universe and everything in it. It is a deeply interconnected and historically contingent search for that truth. What we chose to do with that truth afterwards is up to us, but when we ignore those connections and history and our inability to predict the future, we do so to our own detriment.

  1. Like evolution.
  2. Note that I’m not making the same claim about technology, which as McClellan and Dorn persuasively argue, has had a habit of coming before the science that explains it

Who is Andrew Fabich?

tl;dr: Andrew Fabich is a creationist 'microbiologist' at Liberty University who isn't a great scientist.

Who is Andrew Fabich? This question has haunted me since I watched the debate between Ken Ham and Bill Nye. One of Ham's favourite tactics in that debate was to name-drop 'creationist scientists', as though a parade of Ph.Ds would somehow disprove evolution in a blaze of authority. Most of his name-drops were typical creationists: engineers, medical doctors, and the like. But then came Andrew Fabich. In an attempt to discredit the awesome work done by Richard Lenski and his lab on the adaptation of E. coli to use citrate as a novel food source, Ham suddenly trotted out a microbiologist to take a swipe at Lenski et al.

You can watch the video here, or starting at the relevant section here, but I've transcribed it for you (and so has the Lenski blog here):

Ham: There are those that say 'hey, this is against the creationist'. For instance, Jerry Coyne from the University of Chicago says, 'Lenski's experiment is also yet another poke in the eye for anti-evolutionsts,' he says 'The thing I like most is that it says you can get these complex traits evolving by a combination of unlikely events.' But is it a poke in the eye for anti-evolutionists? Is it really seeing complex traits evolving? What does it mean that some of these bacteria are able to grow on citrate? Let me introduce you to another biblical creationist who is a scientist.

Fabich: Hi, my name is Dr. Andrew Fabich. I got my Ph.D. from the University of Oklahoma in microbiology. I teach at Liberty University and I do research on E. coli in the intestine. I have published in secular journals from the American Society for Microbiology including Infection Immunity and Applied Environmental Microbiology as well as several others. My work has been cited, even in the past year in the journals Nature, Science, Translational Medicine, Public Library of Science, Public Library of Science Genetics, it is cited regularly in those journals and while I was taught nothing but evolution, I don't accept that position and I do my research from a creation perspective. When I look at the evidence that people cite of E. coli supposedly evolving over thirty years, over thirty thousand generations in the lab, and people say that is it now able to grow on citrate, I don't deny that it grows on citrate but it's not any kind of new information. It's .. the information's already there and it's just a switch that gets turned on and off, and that's what they reported, and there's nothing new.

Ham: See, students need to be told what's really going on here. Certainly there's change, but it's not change necessary for molecules to man.

I don't need to deal with Fabich's criticism of the E. coli work, for the simple reason that Lenski and his postdoc Zachary Blount have already crushed it over at their blog post. You can see it here, and I encourage you to do so. It's a great read for the biology alone, and it's pretty damning stuff for Fabich. As Zach says at one point:

Fabich went on to state that this “switch” is what we reported. That is emphatically not true. It beggars belief that anyone, much less a trained microbiologist, could actually read our 2012 paper, where we reported the genetic basis of Cit+, and come away thinking this.

So who is this guy? Who is this Ph.D. in microbiology that makes such obvious and simple errors, who presents himself as a creationist biologist and appears with Ham to misinterpret some great work?

Well, let's start with where he works. Fabich is an assistant professor at Liberty University, which is already ringing an alarm bell. Liberty University is a private Christian university located in Virginia, and its biology department openly teaches Young Earth Creationism (YEC). How about Fabich himself? He made a pretty big deal of his publication record during the debate, so I think that we should start by taking a look at it. Fabich has five publications listed on his profile, all dealing with E. coli and the most recent published in 2011 (a Google Scholar search shows the same thing, disregarding a couple of obvious false alarms). These articles have indeed been cited: 6, 56, 82, 16, and 12 in order of date of publication, but these are all large-team papers, with over a dozen authors for several of them and no less than four. This is not suggestive of a creative and robust scientific output on Fabich's part. Finally, the 2011 paper shows his affiliation as being with Oklahoma, which suggests that Fabich hasn't published a single thing since moving to LU. As far as track records go, it wouldn't get you tenure at Harvard (if that mattered to you). Hell, I have more than double the number of publications that he does.

If that was all there was to it, then I probably wouldn't be writing this blog post. But then, I came across this video. It appears to be another attempt to parade a 'creationist scientist' in front of a camera, but it's interesting for its content. In it, Fabich manages to revise the history of scientific thought, bag on the scientific method, quote-mine (incorrectly) a paper on evolution from the 1960s, and from this conclude that evolution is false. A choice highlight from the middle of the video:

The science is not the issue. When you look in the scriptures, even Jesus acknowledges this when he says in Luke 17 that 'the kingdom of God comes not with observation'. Why would you impose that worldview on me? Even Jesus says that you can't do an experiment to prove God or who God is. So, what is the scientific method. Actually, one of the points that I want to make here, right up front, is that modern science had its foundations in the Bible, in Christian Europe. Okay, there are some exceptions, like some people out in India and Turkey, they're isolated and rare exceptions. But the scientific method is based on Biblical presuppositions. I'm not going to go into all of those, but the scientific method, you realise it, you start out with an observation and then you go and you make a hypothesis, collect your data and then there's oh interpretation. You can't get rid of your bias. All scientists are bias [sic]. I'm guilty and so are you.

So, the problem with science that I have is that it never ends. Well, it might not be a problem, it's how I keep my paycheck. Okay, I get it. So one good hypothesis leads to another and so it goes on and on and on and it never stops. If you're not careful, you get trapped into worshipping the internal scientific method rather than the eternal creator of the scientific method who gave it to us so that we could receive it.

What it comes down to here is, our theory has become one which cannot be refuted. You know who said that? It must be a creationist, some big creationist you all recognise and you've got your short list of who it said. Because we're just, we're uncompromising and we're not based on facts and data. You know who said that? It was Paul Ehrlich and L. C. Burch. They, the evolutionists, said 'our theory of evolution has become one which cannot be refuted by any possible observation'. Are you meaning to tell me that it's not based about facts? Whoaaa, so evolution's not based on fact.

There's so much wrong here that I barely know where to start.

  • The history of modern science doesn't begin with the Bible. It is difficult to extricate Christians and their institutions from the matter, but to say that modern science started with the Bible is laughable at best. For instance, such a statement manages to ignore the entire history of scientific thought in Ancient Greece. Aristotle formed a significant, even commanding, aspect of scientific thought until the Scientific Revolution through the 16th to 18th centuries. It also ignores the important role that Byzantine and Islamic influences played, and grossly trivialises the achievements of civilisations in places like India and China. These are all recorded and established facts that Fabich blithely rolls over.
  • The scientific method is a large part of what gives science its power. And far from being a problem, the recursive nature of scientific progress is one of its greatest strengths. The comedian Dara O'Briain said it well when he said 'Science knows it doesn't know everything; otherwise, it'd stop. But just because science doesn't know everything doesn't mean you can fill in the gaps with whatever fairy tale most appeals to you.'
  • Yes, scientists are biased. We're all human. In fact, if Fabich cared to Google it, fields like the philosophy of science and the sociology of science exist to tackle exactly this question. But in general, the power of science is that it is self-correcting (though this is not without challenges, and needs constant work). And Fabich basically admits to paying lip service to the scientific method to keep a paycheck. I'll let you decide on how that reflects on him.
  • And of course, what would a creationist be without a cherry-picked quote? The quote from Ehrlich and Birch comes from a paper published in 1967 and – despite what Fabich has implied by leaving out the following sentences – is not some sort of anti-evolution screed. In fact, the quote in his video goes on to say: 'The cure seems to us not to be a discarding of the modern synthesis of evolutionary biology, but more scepticism about many of its tenets. In population biology, more work is needed in elucidating the general properties of populations, both those made up of one species of organism and those made up of two or more species without reference to dogmas or guesses about how they may have evolved.' So, in reality, the quote that Fabich has chosen is actually about a call for more empirical work to fill in the gaps in the data. And as anyone who's picked up a book in the last 50 will have noticed, they got what they were asking for. (For a longer fisking of this same quote and others, check out Peter Hutcheson from nearly thirty years ago. Way to stay current, Fabich).

So, who is Andrew Fabich? Well, the evidence suggests that he's a poor excuse for a scientist. It suggests that he's not an active member of the scientific community, and that he's interested not in helping the progress of science but in tearing it down to satisfy his worldview. And it suggests that we can safely ignore him.

But Fabich is only the symptom of a larger problem, one that Ken Ham exploited ruthlessly in his side of the debate. The problem is credentialism, or the over-reliance on credentials such as academic degrees. Ham was simply employing a time-honoured technique: parade out a bunch of 'doctors' and 'scientists' who are creationists in an attempt to get a pass simply because they have Ph.Ds. The problem with this is two-fold:

  1. When verified properly, credentials can be a useful tool in situations such as making hiring decisions (a Ph.D. minimum for a research position is probably a defendable, if not foolproof, criterion to use). But academic credentials are no proof of research savvy or even basic competence; anyone with a browser can surf their way to a Ph.D. at a diploma mill. And the problem with Ham listing scientists who happen to be creationists is that it misses the fact that the vast majority of scientists do not share their beliefs. In fact, Project Steve (of which I am a proud member!) was created to mock this very phenomenon of listing creationist scientists.
  2. Ham is essentially making an argument from authority, which is a logical fallacy. The fact that I have a Ph.D. in Biology doesn't mean that I'm automatically right about anything biology-related, even in my own area. What it signifies is that I've spent a long time studying and thinking about biology and related topics, and that my thoughts on the matter are probably more well-informed than the average person's. But if a precocious seven-year child wanders up to me and hands me a verifiable fossil of a Precambrian rabbit, then as a field we would have some serious re-thinking to do1. It doesn't matter that she's still learning to reliably write her own name, or that I have a Ph.D. The evidence is the evidence; we don't make the case for evolution based on our degrees, we make it based on our observations of the world around us.

You can see this at work with Fabich and the debate in general. Fabich shows up in the video, snows the audience under with his credentials, and then declares – based solely on his now-established authority – that Lenski et al don't know what they're talking about. If you watch the video, you'll notice that Bill Nye doesn't do any of that. What does he do instead? He presents evidence. He holds up physical objects, he shows records of observations of trees and ice cores, he discusses what we see in the Grand Canyon.

So why do Ham and crew do this? Because, unfortunately, it works. This is one of the great challenges of science communication: people don't have the time or inclination to become experts, so they rely on others to do it for them (a mental version of the division of labour). How is the average person to know who has a "real" Ph.D. and who doesn't, or which expert is trustworthy and reflects the broad scientific consensus? Creationists, climate-change denialists, anti-vaxxers: they all rely on the same method of inducing doubt. They agitate for 'balance' and 'teaching the other side', because they know that doing so legitimises the debate. In fact, it's one of the reasons that I don't support Nye's decision to debate Ham. I feel that he did a great job in the situation, but I still think that it was a mistake2.

Until we can find a better solution to this problem, though, we're stuck with how I started this post: we need to root out people like Fabich and bring them into the harsh light of good science. Now if you'll excuse me, I have to go do some science of my own.

  1. We might also want to investigate the awarding of a major scientific prize to a pre-teen, but that's another issue
  2. Though this is arguably an empirical question. I could be wrong. Perhaps, on balance, he did more good than harm.

What evolved first, sight or hearing?

While getting tangentially involved in an unrelated conversation about the science behind evolution yesterday, I ended up getting this great question from J. William Runnells yesterday:

Now, I got all excited and gave it some thought and read a bunch of stuff and even went to the library 1 to respond to this, but before I do, a disclaimer is in order:

This is a complex question, and not something I’ve done work on myself.  I welcome additions, corrections, and even complete overhauls from people who work in this field.

That said, let’s give it a whirl.

  1. Yes, I’m a nerd.  I know, I hide it well.

Slides from recent talks…

I put a fair bit of effort into the design of my talks, so I thought that I would share a couple of the recent talks that have kept me busy as a glimpse into my approach to communicating my science. I’ve done this before, and you may have noticed there what you’ll notice here: over the years, my visual style has evolved (ha!) to be quite minimalistic. I prefer to stand in front of my slides and use them as support, so I keep text to an absolute minimum and focus on using images and short bursts of text to provide emphasis, guide attention, and advance a narrative. This isn’t an approach that will be comfortable or appropriate for everyone; it also makes sharing slides like this a little bit of an odd proposition, because there’s ample room for misinterpretation or unanswered questions when I’m not there to actually talk about what’s on the screen (as I feel that it should be – otherwise, why are you there in the first place?). Thus, if you see something that you don’t understand or that looks odd to you, please give me the benefit of the doubt and feel free to ask questions in the comments!

The first is a talk I gave recently at the biology department at Macquarie, where I was invited by my friends Matthew Bulbert and Julia Cooke. I was inspired by the video games of my early youth, and went with an 8-bit theme:

The second is an outreach talk I gave to a general audience at the Sydney Athiests meetup group a little over a week ago on human evolution, arguing that it has happened, is happening, and will continue to happen. I wrote this talk in a hurry, so I got a little lazy with the font selection (2 points if you know where I got the main font combination in the talk from).

Below are the links to any images that I used, either directly or as inspiration, for these talks which I did not create myself or purchase as stock images. I think I got everything, but if you notice anything missing, please let me know and I’ll try to correct it as soon as possible!

Image links for the Macquarie talk:


Image links for the human evolution talk



Got a nice picture of this fellow (?) when he landed in our back yard for a bit of a perch on our clothes dryer:

The kookaburra – this picture is most likely of a Laughing Kookaburra, Dacelo novaeguineae) –  is one of the largest members of group of birds known as the kingfishers. It is well-known for its distinctive call that, as the name suggests, sounds like a laugh.  You can read more about the kookaburra, and hear an example of its call, at this nice little write-up I found about them here (scroll down on the right hand side to “Calls” to find the audio).

(The kookaburra has also been the centre of a few controversies, mostly related to a popular children’s song about the bird).

Memoir of an academic talk.

tl;dr … well, honestly, go read something else if you don’t like long form.  This is 3600 words of navel-gazing detail, and I’m not about to apologize for it.

A companion piece to my earlier post on the process of designing a poster, this post deals with the talk on the same material for a different conference (vastly different audiences, so I don’t mind overlapping).  As I said for the post on designing the poster, this is a snapshot, or series of snapshots, of my process for doing science and preparing talks.  It’s not the whole picture, and I’m deliberately  exposing the warts and bumps that go with doing science;  I don’t get to control the image you form of me as well as I otherwise might, but I feel that the resulting material is more honest and informative.

In any case, I hope you enjoy it.  Please leave feel free to leave comments or questions, and I’ll do my best to answer them.


– Monday, July 23, 2012:  The ISBE 2012 conference is a couple of weeks away, so it’s time to start thinking about the talk.  The initial steps will be a little slow, but today I’ve created the presentation file as a symbolic step.  I haven’t yet conceived of the overall visual theme of the talk, so for now I’m adopting a simple black  on white approach. 

– Thursday, July 26 4:30 p.m. I’ve got about a half an hour before I need to leave the lab to go meet my long suffering wife for dinner.  Time to outline some content!  I’m working quickly, creating new slides and just typing main ideas of the story I’m telling into them.

– 4:51 p.m. 20 minutes later, I’m done a really quick outline.

A couple of things to note.  First, considering that this is a 12 minute talk, you may be wondering if 22 slides is too much. Yes, and no.  For most people, 22 slides is too many for this length of talk;  a good rule of thumb is – depending on the density of your slides – allow for at least a minute for any slide you’ll be saying more than ‘hello’ over.  This is a mistake that I see people make time and time again:  they make hugely dense slides with dozens of graphs, and then leave themselves about 15 seconds per slide.  This won’t work.  They either end up blasting through slide after slide of results, or they go way over time1 .  Aim for simplicity, and remember that simplicity is hard.  Simplicity doesn’t mean dumbing down your message, it means presenting your message in as straightforward and audience-appropriate2  a fashion as possible.  On the other hand, I deliberately present more slides with fewer ideas on each one;  this is a conscious strategy aimed at controlling what the audience is seeing and thinking about on a more fine-grained level.  However, this is a more difficult approach, and you should be careful about adopting it.  Long story short, if you have more than about 1 slide for every 30 seconds to a minute, you should have a good reason why. Also, the outline is hardly set in stone.  As when I did the poster, it’s an iterative process which will lead to me adding and subtracting material as I get into the content and the design.  I’ve already got some ideas that may add in a few slides, so I’ll probably need to subtract some elsewhere.

– Monday, July 30, 4:36 p.m.  Squeezing in a few minutes to work on the slides before I head for home.  I don’t have a cohesive plan for the design of the slides yet, so I’m going to iterate the content a little and see what suggests itself.

– Tuesday, July 31, 11:30 a.m.  Only got a few minutes in on the talk yesterday before I got distracted by an ‘emergency’ (read: time-suck).  I just realised this morning that I really need to create two versions of this talk, because I’m going to be giving it at a couple places I’m visiting in Europe after the conference.  This means that I need a 12-minute version for ISBE, and a 45-minute-ish version for the seminars I’ll be giving.  This isn’t as bad as it looks, because creating the 12-minute version requires cutting out a lot of material that I would otherwise put in;  while it makes for more work creating slides for the longer version, it’s more relaxing because I can afford to go into details that I would have to otherwise avoid in the shorter version.  This post, however, will focus on the 12-minute version which I will create first.

– 4:20 p.m. It’s been a bit of a slow day, but some of the pieces are starting to come together.  I’ve got a few of the visual ideas worked out, and though there is a massive amount of work left to do, at least I’ve got a direction.

You may notice a few things.  First, I’ve littered the slides with notes to myself explaining where I want to go with that slide, reminders about content to add or delete, and even notations on which notes might be suitable to cut from the final version.  Second, if you look closely, some of these images are decidedly low-res.  That’s because they’re “comps” of stock photos (from iStockPhoto), which are super-low-res versions that are watermarked so as to be unusable in a production document.  They are, however, useful for trying things out and deciding what image works best before you lay down money for the final image file.  This lets me play with the slide deck before committing (an example is the image of the dog and the bat;  I’ll only use one when I discuss rabies, but I’m trying them out to see which I like better), and it might even be possible to find free alternatives to the images I’ve used.  The final thing of note is that I haven’t addressed the typography of the presentation yet;  the font used in the slides so far is Keynote’s default Gill Sans, but my next step is to choose some appropriate fonts now that I have a bit of content in place.

– 2:36 a.m.  I’ve been working for the last three hours transcribing every common name and genus-level-or-above taxonomic name from the index of Odling-Smee et al’s monograph on niche construction in an attempt to set the stage for why I’m giving this talk;  namely, that viruses are under-represented here.  To make this point visual, I’m turning it in a word cloud (you can see the placeholder I whipped up in the slides above).  I’ve reached the T’s and I have to stop now because otherwise I’ll be doing this all damn night.

– Wednesday, 12:26 p.m  Back to it, and I’ve finally finished the index.  Now to throw it into R (using the “wordcloud” package), pretty it up, and insert it into the talk!  (And yes, I *will* go way too far for a detail no-one will care about).

– 1:06 p.m.  Here’s the new placeholder that I’ve created in R.  It’s still a placeholder because I’m going to try to match the fonts and colors to the rest of the slides;  making those decisions is the next step.


– 4:25 p.m.  I’m ‘auditioning’ some font and colour scheme choices.  To do this, I’ve duplicated my presentation and slides with in it, and I’m applying various styles to see how they work.  I’m looking for a bold, attention-grabbing combination, because I want this to stand out from a sea of similar-looking talks;  since I’m not adopting any sort of high-concept approach for this talk (mostly due to a lack of time!), I’m focusing on using typography and colour in a more aggressive way than is usual.  With that said, I could really use my wife’s designer eye on this, because I’m having anxiety attacks over what combinations might work.  I like the use of Bebas Neue and a script font for the headers, but I’m having trouble with a body font (because neither of those choices work well as body fonts).  I’m in a bit of a grey area because the presentation really only has a couple of blocks of text that need to be set, so I need to balance readability with mood.

Incidentally – and this is important – I’ve also been ducking into an unused conference room with a project to try this out on the bigger screens.  Always try your talk slides out on a setup that is as close to the final venue as possible.  You want to make sure that the colour combination that looks great on screen actually works when you project it!

– Thursday, 4:36 p.m.  I’ve been working on the slides throughout the day, in and amongst other things on my todo list.  Today I’ve been focusing on the results section, which has seen some progress.

I’ve made some subtle modifications, including breaking the green color of the palette into a brighter green for text on black slides (like the title slide), and a softer green for backgrounds.  If you compare this snapshot to the previous one, you should be able to see what I mean.  Also, I’ve started redoing my figures to use the fonts that I selected for the talk.  It’s a small thing, and perhaps no-one would consciously notice, but I believe in minimising friction for the viewer;  different fonts and designs between parts of the talk can be jarring even if the audience can’t figure out why, and I want to avoid that as much possible.  It may not be entirely doable (I still have to figure out a better way to present that tree, for instance, and I’m not sure if I’ll be able to find a way to change the font on that), but I’ll go as far as I can to homogenise the design.

– 4:52 p.m. I’ve ducked into the  conference room to check on how the slides are showing up on the screen.  I’m generally happy with it so far, but projecting it makes it clear which version of the word cloud I’m going to keep;  the script version is painful at large sizes.

– 11:04 p.m.  I’m continuing to work on the slides.  I’ve been going back and forth between the bat picture and the dog picture for rabies (another potential example of viral niche construction, methinks), but now it finally occurs to me that the dog picture just doesn’t read well to anyone but me.  So, it has to go.

– 11:55 p.m.  I’m working on a slide that suggests a speculative link between viral niche construction and sociality;  this is based off of work on a cat virus, so I’m using a picture of kittens to illustrate the point3.  My first version, though, illustrates a design issue:  if you use a picture that has eyeballs in them, the rest of the slide has to relate to the eyeline (somewhat similar to the concept of eyeline matching in film editing) or else the viewer gets uncomfortable.


As you can see, the kittens are looking down and I have text above them;  this creates a visual tension that has no reason for being there. Putting the text below the kittens, besides looking bad  because of the shading at the bottom of the photo, also fails because the kittens are all looking in different directions.  Once I’ve identified this problem, I have to find a new photo;  thankfully, the internet seems to be big on cats (who knew?).

– 12:09 p.m.  I’m wrapping up for the night.  I’ve made reasonable progress today:  aside from a set of slides in the middle that I’ve engaged my wife to do drawings for, the last thing that I need to do for this first, rough version is to redraw the phylogenetic tree and find a way to present it.

If you’re paying attention, you’ll notice that I’ve still got too many slides.  I’m going to be practicing this talk (including a lab practice talk next week), but it’s almost certain that I’m going to need to cut some material.  Like any other content editing, there’s going to come a point where I have to kill my darlings. This doesn’t bother me as much as it normally would, because most – if not all – of what I cut will end up going into the longer seminar version of this talk, where I’ll be making the same case in greater depth.  You can see that I’ve already started doing this, as I’ve moved some slides after the acknowledgements at the end;  these will be included in the longer version unless I cut them entirely.

- August 6, 2:26 p.m.  I’ve been fiddling with the slides over the last few days, just trying a few things out and moving things around.  I’ve decided on one of the cat photos, the middle one, as it’s the most engaging; my wife pointed out that this is because of the way they’re looking, including the one staring straight at you.  I’ve got her working on producing a diagram for me to explain the way baculovirus manipulates its hosts, which goes in the blank spot in the middle, and I’ve placed images in there to help get me over the hump.  Today, I need to fix the phylogenetic tree and place it in;  whether I use it in the short or long version, I’ll need it at some point.  And I want to get the short version done tonight if I can, because I plan on practicing it tomorrow before I present it to the lab on Thursday.  So here’s the current state of affairs:

– August 7, 2:15 a.m.  Small refinements now.  Unfortunately, even in consultation with my talented wife I couldn’t come up with a good illustration  for the slide I’ve been holding on the various genotypes;  thus, I’ve decided to break down and use (gasp) text.  I know, I know.  In the mean time, I’ve also managed to refine the tree diagram (which requires further refinement, but the pieces are there now).

– 1:02 p.m. I’m searching for images to illustrate the hypothetical genotypes (zombie, non-gooey;  non-zombie, but gooey).  I’m having trouble meeting the criterion of Creative Commons or stock that I can purchase as well as being the right image for the idea.

– 3:02 p.m. I’ve found images and replaced the phylogenetic trees. I’ve also replaced a slide that I apparently deleted at some point along the way without noticing;  you’ll notice that the second slide in the talk is missing if you compare the last two snapshots above.  Using OS X’s Versions, I was able to graphically browse to an old version from a couple of days ago, find the slide, and drag it and drop it directly into the current version of the talk.  It may not be git, but it’s still cool.  And it’s also a good lesson:  keep old versions!  Keep backups!

I think that the short version of the talk is in good enough shape now that I can practice it, so I’m going to go see if I can find a room with a projector to play in.  If you can, it’s best to practice talks under conditions that are as close to the real thing as possible;  that means standing up in front of a room, even if it’s empty, and playing your slides behind you as you address the room.  Muttering under your breath as you stare at the slides may seem like a good way to practice, but you’ll never find the timing problems and flow issues unless you force yourself to stand up and actually talk.

– 4:52 p.m.  I just finished practicing my talk for the first time.  As I expressed on Twitter:

Seriously, people.  Practice your talks before you give them.  Then, practice them again.  And then three more times.  What I’ve learned is that I need to do some rearranging, because the flow of ideas in the talk didn’t quite work;  I’m going to jettison a few slides and use them in the longer version, and I’m going to see if I can add a few elements to the text that I abruptly noticed were missing.

– August 8, 12:24 a.m.  I’ve spent some time rearranging slides and writing down what I want to say on each slide.  I like to have my material memorized to the point where I can present it without notes, but I sometimes find that writing down key points of each slide when I’m practicing helps me to achieve that goal.  Here’s the current state of the short version, with changes incorporated.

I’m still struggling with some aspects of the design.  In particular the genotype slide (slide 17) is bugging me;  I had to add the model diagram because it was too difficult to explain the genotypes by referring to the parameters alone.  Now that I think about it, though, I may try playing with text instead spelling out the assumptions.  But that can wait until tomorrow, because I need some bloody sleep.

– 11:49 a.m. Back to the conference room to practice again!

– 12:42 p.m. I tried it three times, but I’m still coming in too long.  The talk is supposed to be 12 minutes with 3 minutes for questions, and I’m clocking in at 18-19 minutes.  It looks like I’ll need to pare some things down to put into the longer version.  It breaks my heart, but I think that I’ll have to put the word cloud into the longer version;  it’s a great image, but under time constraints it’s not pulling its weight.  When that happens, you need to kill your darlings.

– 1:07 p.m.  I’m cutting it to the bone, but I’ve got things down to 20 slides (simplicity is hard).  The room I was using is booked right now, I’m going to have lunch and do some work until it’s open and I practice again.

– 4:35 p.m.  I’ve practiced this thing backwards and forwards, but I can’t get the time down!  From 19m 28s to 14m 12s, I’m still two minutes over.  I may have to remove the phylogenetic results, though it kills me to do so.  I know that they’ll be in the longer version where I’ll have plenty of time to go over them, but it still pains me.

– August 9, 12:49 a.m.  I’ve spent the last couple of hours finalising the design, including replacing all of the comp images with the full versions that I’ve purchased.  It’s pricy ($86 AUD for 50 credits on iStockPhoto), but worth it.  If you can’t afford to pay for good images, then find them under a Creative Commons license on Flickr, or take them yourself.  But always use high-resolution images!  And don’t steal them.

– 11:58 a.m.  Okay, further practicing yields no advances.  I’m going to have to cut the phylogenetic results in favor of asking people to talk to me if they’re interested.

12:45 p.m.  11 minutes, 58 seconds!  Finally, we’re ready.  Here’s the state of the talk before I give it to the lab this afternoon.  Don’t forget that I’ve got extra slides tacked on (after the slide with the big Thanks! on it).  I’ve also added a slide with photo credits;  again, acknowledge your sources and don’t steal other people’s work.

– 4:45 p.m.  Well, I gave it to the lab (and a distinguished visitor!), and things went pretty well.  It’s clear that the work I put into the design and practicing the talk has paid off, because I received multiple comments that it was a very polished talk.  There were some good questions, and a couple of good suggestions for minor improvements, but otherwise it’s done and dusted!

- August 11, 12:39 a.m.  I leave for the conference tomorrow afternoon, and I’ve just thrown my talk files onto my USB drive – and I’ve got them in my Dropbox, on my iPad, and in my email. You only have them in one place?  You’re begging for a disaster.  But, I digress.  At this point, it’s worth reviewing the lessons I learned while designing this talk.  First and foremost, as I wrote above, simplicity is hard, and you have to be prepared to kill your darlings.  I had more content than I could present, so I had to cut it down and make it as simple as possible.  Practice is king.  I practiced this talk no fewer than eight times to an empty room, and it paid off;  the people I finally gave it to were impressed at how fluent I was.  What they didn’t see was the hours I spent stumbling and swearing and fumbling my words.  If you suck in private, you’ll be great in public.  And finally, iterate, iterate, iterate!  To make good posters and good talks, you need to advance and revise, create and critique.  If you scan back through this post and look at nothing but the slide pictures I’ve included, I hope that you’ll get a feeling for this.

So, if you’re still reading after all of that, thanks for sticking with me!  I hope you learned a little something, and I welcome your thoughts.  But for now, I’m off to Sweden!

  1.  A minor rant:  if you go over on time on your talk at a scientific conference, you are being rude.  You’re holding up other presenters, you’re making it difficult for people to get between talks on time, and you’re generally making things worse for everyone.  I don’t really care about your excuses, because 95% of the time what they boil down to is ‘I didn’t care enough about my audience’s time to practice my talk and make sure that I could present it in the time allotted’.  I’ll cut students a little slack, but only because I’m going to whack their advisors over the head.
  2. What do I mean by ‘audience appropriate’?  I mean that you need to think hard about your audience and explain things they won’t be familiar with while avoiding long digressions on topics that are well-known to your audience.  Spending two minutes defining ‘genotype’ to an audience at a genetics conference will be a waste of your time, but it might not if you’re presenting to a science outreach high school event.
  3.  Yup, that’s right, kittens.  If that makes it into the final version for ISBE, I pity the poor fool who has to follow my picture of adorable kittens

Hey, lots of biologists love math!

Do biologists hate math?  Are they frightened by equations? I was amused to see this paper [zotpressInText item=”NBKZ56XJ”] going around on Twitter …

.. and even more amused when I followed through to see that a friend, Tim Fawcett1, is the lead author on this paper.  It’s already getting some awesome headlines (“Too much math is tough for biologists“, “Math anxiety in school? Scientists have it too“, and my favorite: “Scientists Struggle With Mathematical Details, Study by Biologists Finds“), so I clicked through to see what the fuss was about.  It turns out that it’s a sensible discussion on how to encourage more cross-talk between empiricists and biologists;  they analyse the number of citations papers receive as a function of their ‘equation density’ (equations per page), and find that there’s a sharp drop in the number of citations that a paper receives as the number of equations increases.  Not all is lost, though, as they discovered that equations in an appendix don’t have this effect, leading them to suggest a reasonable compromise:  move the bulk of the mathematical detail to an appendix for readers so inclined, and put careful focus on clear explanation of the model and its assumptions in the main text.  I read theoretical papers for a living, and I have to agree wholeheartedly with their suggestions.

With that said, I shudder to think at what the media is going to do with this one.  There’s already a vague perception that biology is just stamp collecting, and even xkcd took a poke on this topic a while ago:

But the truth is that biology is full of interesting mathematical challenges and mathematically astute people (pick up just about any text on mathematical biology, epidemiology, population genetics, etc. to see what I mean).  Tim and Andrew are simply commenting on the need for more integration between theorists and empiricists, with a sprinkling of eminently useful advice on how to get that done.  I’m curious, though:  do you think that it will get cited?


Update (10:39 p.m.): I’m wondering if EurekAlert might be the source of some of the weird headlines I’ve seen about this paper, like this TGDaily article that’s no longer just talking about biologists shaking in their mathematical booties – they’ve moved on to ‘scientists’.  The EurekAlert article talks about ‘scientists’ and, oddly, links the problem to Hawking (I’ll bet those pesky physicists will be distressed to learn about how scared they are of math…).

Update 2 (10:45 p.m.): Just noticed that the Science Careers blog points out the weirdness in the EurekAlert article too.  This is, in itself, a little strange since both the Science Career blog and EurekAlert are arms of the AAAS, the association that also publishes the journal Science.  Also, I lol’d at this line: “So what should biology researchers do? Avoiding equations in science–even biology–probably isn’t a good idea.”  Even biology, huh?


  1. Full disclosure: I have a paper in press with Tim, and though I don’t know his co-author Andrew Higginson, I know of him and have a sense that he’s a sharp cookie.

Yes, you could inherit a ‘gene’ for celibacy.

I really enjoy Neil deGrasse Tyson’s work as a science communicator and all-around advocate of rational thought, and I think he’s a really smart guy.  But even really smart people can be fooled when it comes to genetics and evolution, especially if it’s not what they do for a living.  Here’s what Neil tweeted this morning (my time):

Unfortunately, that statement just isn’t true.  There’s a couple of possible explanations, because his statement (despite being ‘simple logic’), is a little vague and open to interpretation.  It’s possible that he was talking about an allele for celibacy, with the other allele probably being the ‘has sex’ allele.  However, as several people pointed out on Twitter, if the ‘celibacy’ allele was recessive it could easily be inherited.  Another plausible scenario that I didn’t see anyone on  Twitter catch is that it could be caused by overdominance (or heterozygote advantage);  just like the case of sickle-cell anemia, where homozygotes have reduced fitness but heterozygotes have an advantage due to their resistance to malaria, if a double dose of ‘celibate’ reduced fitness but a single dose led to greater fitness for some reason then celibacy would be maintained.

More generally, we can ask how a trait like celibacy could arise by evolutionary forces (if indeed it did, and wasn’t simply a cultural artifact).  In order to – hopefully – eliminate the effects of culture, we’ll consider an animal model in which some proportion of the population is celibate.  How could that happen?  Well, if you consider the question in its more general wording as “how could a trait that leads to animals failing to reproduce arise”, the underlying logic is much the same as for same-sex behaviour in animals.  Celibacy would be a more extreme form of this general question, as not many species have members with exclusively homosexual behaviour that have zero chance for reproduction (though apparently there are a few examples, such as sheep), but if an adaptive or non-adaptive explanation works for the persistence of homosexual behaviour then it might work for the persistence of celibacy too.

Helpfully, Nathan Bailey and Marlene Zuk wrote a great review paper a few years ago (here’s a pdf link I found) that rounded up many of the potential explanations for same-sex animal behaviour.  Looking at Table 1 of that paper, where Bailey and Zuk list the explanations in short form, it’s clear that some of them don’t work for celibacy (like the idea that same-sex behaviour is selected for because it provides practice), but several of them do work.  The most obvious potential explanation for persistence of celibacy would, of course, be kin selection.  If a gene for celibacy conferred indirect fitness benefits (i.e. if celibate individuals enhanced the fitness of their sibling), then that gene could be selected for and lead to a polymorphism in the population.  Celibacy could even be a byproduct of the evolution of life history traits, especially in humans where advances in survival and resource provision have led to greatly reduced birth rates as individuals rationally put more and more effort into fewer and fewer offspring to maximize fitness;  if genetic variation for this trait were being maintained and the optimal number of children was low, it  could lead to some individuals ‘overshooting’ the optimum and having zero children.

These are, of course, simply wild speculation dressed up in elements of evolutionary theory, but they are still plausible explanations for how a ‘gene for celibacy’ might arise.  Don’t mistake them for likely explanations, mind you;  even if we do manage to ignore cultural effects which almost certainly play some kind of  role in human celibacy, many of the plausible explanations for celibacy like kin selection have received little support in terms of same sex behaviour (as Bailey and Zuk note).  The reason I bring them up here is to illustrate a specific point, i.e. that seemingly simple statements about evolution can be surprisingly wrong.  Even if you’re as smart as Dr. Tyson.

Now that we’ve found Nemo, it’s time to save his friends.

Nemo! Picture by Peter E. Lee, used under a CC license.

There’s many things that we don’t know about the ocean, and most people won’t find that too surprising, but what might be surprising is the extent of our ignorance in some areas.  This is the subject of a recent paper by McClenachan et al. in the journal Conservation Letters, entitled “Extinction risk and bottlenecks in the conservation of charismatic marine species.”  The problem, they contend, is that while the oceans are currently undergoing a massive loss of biodiversity, the full picture of that loss cannot be seen because we’re not even close to knowing how many species have been lost or how many are currently threatened with extinction.

As a small first step to dealing with that issue, the authors of this paper examine marine charismatic species as a way of estimating the threat to some of those species and identifying possible impediments to their conservation.  What are charismatic species, you ask?  They’re species with widespread appeal that receive more attention and funding for conservation (some might say too much attention and funding);  it’s suggested that charismatic species can raise awareness and drive conservation goals.  In this paper, the authors leverage the fame and fortune of marine charismatic species by arguing that because they receive special attention and are – theoretically – at the least risk of extinction even when threatened, charismatic species can serve as an estimate of the lower boundary of the probability of extinction.

The paper takes an unusual and amusing tack to do so.  In their own words: “we summarize the extinction risk of 1,568 species within 16 families of well-known marine animals represented in the 2003 Academy Award-winning movie, Finding Nemo“.  It’s not many papers in which you get to start “with all major characters, as defined by those with credited speaking parts”, including all species in their taxonomic families which included invertebrates, bony fishes, elasmobranchs (sharks and rays), birds, and turtles.  You can follow through the paper for the exact details of how they constructed the lists, but they then took that list of species and evaluated their risk of extinction.  Following that, they evaluated the potential bottlenecks to conservation among the various families. There’s a lot of fascinating detail in this paper, but I’ll skip to the punchline and let you read the rest for yourself.  For me, the most interesting aspect of this paper is captured by Figure 3:

Here we see that many species, especially in the invertebrates and fishes, are almost entirely ignored either in terms of scientific effort (here the number of papers published on the species), status evaluation (are they endangered?), or conservation assignment (listed by CITES, the species-protection for threatened species).  The authors point out that the charismatic species like turtles and birds receive the bulk of the attention at every level, while conservation bottlenecks arise in the other families.

The focus on Finding Nemo is an amusing hook, but though the paper deliberately trades-off rigor for rhetorical power, the argument that the authors make is a clear and important one.  In calling for a greater focus on the marine biodiversity being lost before our eyes, McClenachan and her coauthors make a great point and deserve the attention that they received for publishing this paper*.

Having said all that, there’s a lot left that to talk about regarding the issues that this paper raises.  In particular, I’m struck by the elements of economics, social psychology, and sociology that would interact with the conclusions of the authors’ work.  The fact is that conservation is, and probably always will be, a finite resource (limited in part by money, and in part by scientific personnel) that must be spread about the overwhelming number of species that are likely to be threatened.  This isn’t to say that the status quo is right, or that we shouldn’t strive to improve it – quite the contrary.  But even in the best of all possible worlds, the fallible human beings tasked with the goal of saving these species (scientists, polticians, the general public) are going to exhibit biases of cognition and simple attention that may make it difficult to drum up support for, say, many of the invertebrates in the paper’s list of species.

Take another look at Figure 3 and try to imagine reasons why some of these species might be relatively ignored.  Off the top of my head, a few potential hypotheses jump to mind.  Physical features of the species’ in question may play a role;  for instance, simple preference for anthropomorphism could account for some of the attention paid to the charismatic megafauna.  It’s easier to care if you can imagine the animal talking but it’s a lot easier to imagine a talking shark or clownfish than a talking shrimp (and don’t discount preference for neoteny;  this paper by Mark Estren looks like a good read on that subject).  Or, even something as obvious as size could play a role:  it’s a lot harder to find or pay attention to many of these marine invertebrates than the turtles or sharks or birds that they compete with.

Even the sheer number of species involved could be important, in more than one way.  On one hand, the fact that there are 6 species of turtles compared with 536 species of invertebrates in this paper seems relevant, as the sheer effort involved in finding and cataloguing the marine invertebrates is daunting.  On the other hand, I’m also reminded of work in economics by people like Barry Schwartz and Sheena Iyengar on the paradox of choice:  when confronted with too many options, people are unhappy and find making decisions difficult, even though they claim that they prefer to have more choices available to them.  The number of possible targets in marine invertebrates for conservation efforts could drain the will of politicians, the attention of the public, and the interest of new grad students selecting a species to work on.

I wouldn’t be surprised at all to hear that the people involved in conservation work have thought about some or even all of these issues, but I would not hesitate to recommend a multidisciplinary approach to this problem.  The answer to the call put out by McClenachan and her co-authors has to include a sober analysis that maximizes the efficiency of the resources we have while, perhaps, searching for innovative new ways to increase those resources.  Here’s one thought:  maybe it’s time for a Kickstarter for conservation – a ConservationStarter?  If the idea of a charismatic species is to reach its fullest expression, I can imagine that it might be in the form of directly crowdfunded conservation efforts targeted at particular species.

Whatever we do, the authors of the paper make it clear that we have to do something, and that our actions have to start with knowledge.  There’s simply too much out there that we don’t know;  we may have found Nemo, but we don’t know very much about his friends and we’re in danger of losing them too.


Loren McClenachan, Andrew Cooper,, Kent Carpenter, and Nick Dulvy (2012). Extinction Risk and Bottlenecks in the Conservation of Charismatic Marine Species. Conservation Letters, 5:73-80.

* My post isn’t especially timely when it comes to this paper, as it was published in January, and others have written about it before me;  a good example is the fine folks over at Southern Fried Science or the Scientific American blogs.  However, the paper was only recently brought to my attention by the good folks in Bill Sherwin’s lab, and the discussion we had about it inspired this blog post.