Monthly Archives: April 2012

Congratulations, Alberta! Uh, I think….

Well, the CBC has called it:  Alberta has elected a Progressive Conservative government.

I never thought that I would be vaguely happy to hear that my home province has elected a Tory government;  they’ve been in power for over 40 years now and I would have been happy to see a change, but I am glad that the homophobic, racist, anti-science Wildrose party hasn’t taken power.   And the fact that Alberta has now elected its first female premier is something that shouldn’t be ignored or minimised.

What I’m still upset about, though, is that Alberta has decided to put the Wildrose party in second place, crushing the Liberals and NDP by comparison.  Danielle Smith wouldn’t be out of place running along side Sarah Palin, and now she’s forming the official opposition in Alberta?

For shame.

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Hurrying to go to better things.

Over at Why Evolution is True, Jerry Coyne addresses an article by Andrew Riggio, in which Riggio questions the thought processes of a man named Paul Lord who thanked God for saving him from a tornado that struck in Oklahoma, killing several (including 3 young girls) but sparing him.  Noticing that (unsurprisingly) the comments have exploded into a sprawling mess, Coyne pulls out a few for special attention including this one:

Kleb  •  22 hrs ago
Wooooooow. Bitter much? The author’s argument presupposes that from God’s point of view death is bad. People of “true faith”, as his last sentence mentions, are equally grateful to God for His providence in death as in life. Look at the great heroes in Christianity. When they died they weren’t bawling and begging God to spare them, they were profoundly relieved to be joining Him and, at the same time, deeply grateful for the ride they had been on in this world. From a Christian perspective, then, there is no inconsistency here. The survivor is grateful for the life God has given him here, as he should be, but that doesn’t mean he isn’t also looking forward to meeting the Lord.

Whoa!  Should we be grateful to God for asking 6 million Jews to join Him during the Holocaust?

Seeing this reminded me of something I read a while ago in John Aberth’s great book Plagues in World History.  Faced with the crushing mortality and morbidity of the First Plague (the Justinian plague that ran from roughly 541 to 750 CE), Christian preachers responded the only way that they could, from the pulpit.  In reply to the bubonic scourge, Aberth notes this particular line of thinking:

By the seventh century, sermon cycles were being compiled to be recited on a regular basis whenever plague struck a region as part of the Church’s now standard response to urge its flock to repent in the face of God’s wrathful chastisement;  this at least is the overarching theme of four homilies composed at this time in Toledo, Spain, which, as expected, are replete with quotations from the Old Testament.  Yet, one sermon, the third in the series, adopts a strikingly different tone by employing the carrot rather than the stick […].  In a remarkable passage, one that seems to be inspired by the New Testament, in particular the letters of St. Paul, the preacher now dangles the promise of immortality during the Christian afterlife or resurrection in order to help his listeners conquer their fear of imminent death from the “groin disease”:

But what should we say?  You who take fright at this blow (not because you fear the uncertainty of slavery, but because you fear death, that is, you show yourselves to be terrified), oh that you would be able to change life into something better, and not only that you could not be frightened by approaching death, but rather that you would desire to come to death.  When we die, we are carried by death to immortality.  Eternal life cannot approach unless one passes away from here.  Death is not an end, but a transition from this temporary life to eternal life.  Who would not hurry to go to better things?  Who would not long to be changed more quickly and reformed into the likeness of Christ and the dignity of celestial grace?  Who would not long to cross over to rest, and see the face of his king, whom he had honored in life, in glory?  And if Christ our king now summons us to see him, why do we not embrace death, through which we are carried to the eternal shrine? For unless we have made the passage through death, we cannot see the face of Christ our king.

(emphasis mine)

Kleb the commenter has one thing right:  a belief that death is acceptable and even preferable to this life, whether from God’s point of view or from the worshipper’s, is certainly not a new phenomenon.  I wonder at the power this line of thinking must have held when those who contemplated it were faced with a disease that can kill 60-90% of those it infects and may have wiped out as many as 25 million during the Justinian plague alone.  In the mean time, though, I’ll be thankful for the efforts of modern medicine and science which have brought the plague to its knees. (Even if we are on the verge of squandering that advantage and resurrecting the plague’s power through antibiotic abuse, but that’s an entirely different post).

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.

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Do you know this bird?

Google has failed me (even the reverse image search, which failed rather spectacularly), and since it worked so well last time, I thought I’d ask the readers once again:  any idea what species this bird hails from?

It was spotted while at the walk-in aviary near Canberra, surrounded by dozens of species of parrots, cockatoos, finches, and more.  But there was no picture on the board identifying it, and I forgot to ask on the way out.  So, if you know this bird let me hear about it in the comments!  A prize will be given for the first correct answer*.

* The prize is a lie.  There is no prize.

Update:  pete chimes in below with what I think is the correct answer:  the Rose-ringed Parakeet (Psittacula krameri) found in Africa and Asia according to Wikipedia.  The internet FTW!

The Rose-ringed parakeet, with a colour mutation to blue...


Rejection Watch Vol. 1, Supplementary Online Material

Photo by Troy C. Boucher Photography, used under a CC license.

Submissions for Rejection Watch have dropped off, which doesn’t really surprise me;  the traffic on this blog isn’t quite strong enough to sustain a feature like that (yet!), though I don’t regret the attempt.  The submissions I did get were fantastic and if anyone out there still wants to send me material, I’ll be happy to resurrect it whenever they do.  In the mean time, though, a couple of relevant posts from around the web have cropped up in the last day or so, and I feel like they make great supplementary reading for those of you reeling from academic rejection.

Rosie Redfield (she of debunking-#arseniclife-fame) over at RRResearch posts her rage over a crappy review of her postdoc’s paper:

We finally (after two months) got the reviews back for the postdoc’s manuscript about DNA uptake bias.    It’s a rejection –  the reviews were quite negative.  The first reviewer was very unfair; they didn’t find any fault with the methods or data or analysis, but they attacked our brief discussion of the functional evolutionary context of uptake bias.  This is all too common for my papers.  The reviewer is so hostile to the idea that bacteria might take up DNA for food that they don’t focus on the science.  Because the paper was rejected we don’t get to do an official response to the reviews, so I’m relieving my frustration by responding to them here.

She goes on to do a detailed, blow-by-blow response to the objections of the two reviewers.  The whole thing is a great read, even if you’re not in this field;  the feeling of ‘oh, that happened to you too?’ is too good to pass up.

Meanwhile, over at The Bug Geek Crystal has found a new pit of despair:

So you know that I handed my draft manuscript in to my advisor last week.  He sent back a document covered in red ink. Then my labmates pointed out all the dumb things I did, and showed me all the cool things I COULD have done but didn’t.

My advisor, a real funny guy, said, “You should make a new graph about the revision process,” and I was all, “Ha ha ha that’s so funny.”

The graph she makes is pretty awesome, but one of the things that struck me was that even the most well-meaning revisions from people close to you (advisors, labmates, colleagues you respect) can cut deeper than the blunt hammerings of an anonymous reviewer with a grudge.  I think that this is because it inspires different emotions, rage for reviewers and despair for labmates.  When we have a personal relationship with those who have dripped red ink on our work, it’s hard to avoid  the attack on your sense of self:  this person knows me, and didn’t think my work was perfect, so there must be something wrong with me.  I should have done better, screwed up.  These are people that you (usually) like, that you want to look smart in front of.  Contrast Crystal’s feelings of despair with Rosie’s feelings of rage;  when anonymous reviewers trash our material, unless we think that they’re right we can work up a really good mad and use it as fuel to revise. In the academic setting, it feels to me like rage is a more productive emotion, a provocation to defiant action (‘I’ll show you Mr. Anonymous Reviewer who will never read this paper again!’) while despair has a soporific effect that leaves us drained and dragging ourselves through the revisions.

Of course, this is just a sweeping generalisation based on my own experience that is almost certainly wrong in some fashion.  But hey, maybe you can leave an anonymous review?  Then I’ll show you.


A quick follow-up to DolphinGate: cool science!

One of the things that surprised me about the weekend’s DolphinGate flap was that most of the mainstream articles I read were acting as though the paper that they were wildly misinterpreting was providing the first evidence for dolphins engaging in same-sex behaviours.  The Huffington Post is a great example of this;  here, for example, is the first paragraph of their story:

Dolphins were once humorously alluded to as “gay sharks” on an episode of “Glee,” but a new study suggests that bisexuality and even homosexuality among the marine mammals may be very much a reality.

I’ll admit that this caught me off guard, because I was under the impression that the dolphin same-sex play was a well-established fact.  How was everyone reporting this as a big surprise?  Yet when I spent a few minutes poking around on Google Scholar, I couldn’t immediately find a good reference for when this was first talked about in the literature.

Thankfully, the internet provides all!  Justin Gregg of the Dolphin Communication Project mentioned my piece on Twitter and, seeing an opportunity to get to the bottom (?) of this, I reached out to ask him if he knew when these behaviours were first observed.  Justin came through in a big way:

1948!  I can’t get at the actual paper (#icanhazpdf?), but the abstract is a gem of scientific understatement:

A summary of observations of captive porpoises is given. Vision and hearing are well-developed, and vocalizations are produced in the form of “jaw-snapping,” whistling, and barking. In captivity the porpoise shows a diurnal sleep cycle. There is a stable dominance hierarchy. Both homosexual and heterosexual behavior has been observed, as well as masturbation in the male. An instance of live birth is described. The play of the porpoise is complex and goes on for long periods. They manifest many and definite fears. The homologies of these types of behavior with that of other mammals is discussed. When various characteristics of porpoise behavior are considered and compared, the animal may be located at many different points in a scale of phylogenetic complexity. Although no information is available on problem-solving in this form, other types of behavior place the porpoise at a place in the developmental scale between the dog and the chimpanzee.

I’ll have to own up to my own foibles here, though, because the conversation may have gone a little down hill after that.

[Insert your own jokes here….]

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