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

Your customer retention strategy isn’t working.

angry(?) giraffe portrait

Adam Foster via Compfight

I’ve been trying to cut my digital costs lately by consolidating my various hosting services in one place;  the blog, Breaking Bio, the audio hosting and feeds for the podcast and the steps I’m taking towards open science.  To do this, I’ve recently been building out my own server on a DigitalOcean cloud VPS1.  So far, the experience has been great … except for cancelling my old services.  HostGator in particular, though, has attracted my wrath.  Instead of just allowing you to cancel your service and then letting the matter lie, they’ve insisted on opening a support ticket, sending me multiple emails asking me to call them (or email if that’s not possible), and finally calling me at home to try and sell me on a year’s renewal at a discounted price.  Here’s the last one I got after the phone call that woke me up this morning:

Hello Steven,

I called you to discuss my offer, but unfortunately I was unable to reach you. So I left a message asking if you could call me back or reply to this email.

I read your cancel request and I see that you want to close your website for a better price. I’m sorry to hear that you want to cancel your service with us due to price. So I would like to offer you a 25% discount off your next invoice. But for the best deal, It would be best if we adjust your billing cycle to 12 months or more with the 25% discount.

I want to do everything I can to help you succeed, so please reply to this email or give me a call. If I’m available I will help you personally, or you can work with any of my team mates. We are here to help you.

John T

I am personally available 10AM – 7PM CST Monday – Friday, you can use Time.IS/Houston to tell you if I am available.

Frankly, I don’t need this.  What I do need is to cancel my service with them in a clean fashion.  If they had such great prices to offer me, why didn’t they offer them when I signed up?  Oh yeah, because they want to charge you more and then dangle the carrot when you realise that you’re getting shafted.  So, I may have gotten a little … agitated in response.  Here’s what I wrote back:


I’m sure that you’re just a guy, doing a job. So I’m trying to avoid becoming angry at you personally. But now, instead of simply cancelling my service as I asked, HostGator opened a ticket, sent me multiple emails, and finally woke me up on the only day all week that I have to sleep in with a phone call I didn’t want.  I was reasonably indifferent to HostGator before this; not a spectacular company, but the product was serviceable and for the most part you guys stayed out of my way. However, at this point, your ‘customer loyalty’ and ‘retention’ program has angered me to the point that I will actively discourage people from using your service. In fact, later today I plan on posting this to my blog (which I now host elsewhere!) to leave a permanent record of this interaction for the world to see.

As to the stated reason for leaving HostGator, price was simply a convenient excuse, like a hastily placed phone call from a friend to allow one to end a bad date. I’m cancelling with HostGator because I’m now hosting with a cloud VPS service that gives me more control, better service, a more attractive interface, and costs half of your cheapest plan with the ability to scale my server(s) at a moment’s notice with complete flexibility. The company that you work for, John, is a lumbering dinosaur. You may feel like Microsoft circa 2000 now, but look how that turned out for them.

So, in conclusion: no, I don’t want a 25% discount on service I don’t need, locked in for a year (subtle move, that). What I want is for HostGator to cancel my service as I asked for in the first place, without me needing to answer phone calls and respond to emails. Perhaps, now that I’ve wasted twenty minutes of my day replying to this, HostGator will finally believe me that I no longer want your service. (And no, I’m not making an international call to tell you this personally, either).

As for you, John, I hope that you don’t take any of this personally. I like to imagine that you’re an honest, hardworking guy who’s just trying to get by; maybe you’re a college kid squeezing out some extra cash so he can do something fun this weekend, or a family man trying to put food on the table. Or maybe the ‘Houston’ thing is a misdirect, and you’re a friendly fellow working at a cubicle in Mumbai. If so, hello! I hope to have the chance to visit your country some day. In any case, I urge you if your life affords you the opportunity: find a new job. Because if their ‘service’ as I cancel my account is any indication – and I believe that it is – HostGator is not long for this world. Get out! Get out while you still can!


Steven Hamblin.

It’s pretty unlikely that anyone at HostGator will ever read this, but if they do:  you’ll probably say that you do this because it works.  And you’re possibly even right.  But one important lesson that companies have learned (or failed to learn) in the past few years is that people don’t like to be locked in.  If you make a good product, they’ll use it.  If they want to switch products, then you should make it easier.  If you don’t, all you’re going to do is make them angry, like you did me.  Now, instead of recommending HostGator to someone else as a reasonable way to host a website for novices, I’ll tell them the truth:  that it was okay, but when I tried to leave they made it a pain and I wouldn’t ever use their services again.

Is that the message you want me out there sending?

  1. Server in the sky.  Like having your own Linux box, but someone else takes care of 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.

Quick and dirty: importing from Bibdesk to Mendeley


My bib files are starting to get a little hairy and I’d like to use some my devices to read papers and sync directly on the go, so I’ve been considering giving a service like Mendeley another shot (though I’m still deeply skeptical of Elsevier’s role in the project1.

When I went to go import my bib file to Mendeley, though, my local files were all left behind.  I use Bibdesk to manage my bib files, and though the resulting import of references went well, all of my linked pdfs were missing.  This is apparently a known issue with Mendeley’s import from Bibdesk, and it doesn’t seem to have been fixed.  Meanwhile, people have come up with workarounds and some have been posted (e.g. here), but I couldn’t find one that worked out of the box (especially since Bibdesk changed to base64 encoded urls a while ago).

  1. For another view, we interviewed William Gunn from Mendeley a while ago on Breaking Bio.

Nobel prize or GTFO.

After reading this great and thought-provoking post by scicurious on ‘failure’ in academia, I came across this comment (which was itself a reply to another comment):

Jenna, with respect, this is a description of how to do incremental science – but it’s NOT how discoveries are made. Not big discoveries, anyhow. Big discoveries DO require inherent creativity and vision .. and we are systematically weeding those qualities out of biomedical science, thanks to the hyper-conservatism exercised by NIH panels.

Please, go read Thomas Kuhn. I’m begging you.

Allow me to respectfully present the opposite view: please don’t read Kuhn. Or at least, don’t read him with the wide-eyed adoration that he’s afforded. Kuhn was dangerously anti-scientific and I place at his feet a great number of the current structural problems with science. His disdainful view of plodding ‘normal science’ and focus on revolutionary ideas is – IMO – a direct precursor to what I might call the ‘Nobel Prize or GTFO’ disease that permeates science now. You either get the cover of Nature and Science, or you’re a waste of time as a scientist.

And what’s wrong with incremental science? For one thing, it’s the way that a lot of science is done. As James Franklin1 points out, fields like ornithology or oceanography work on the incremental accumulation of knowledge and aren’t prone to paradigm shifts. Are they not science? Have we learned nothing from the explosion of scientific fraud in recent years as people are forced to come up with ever-sexier results or lose their funding? Or the recent push for replication, is that just plodding normal science? Kuhn makes us feel good – if no one’s listening to our ideas then it’s not because they’re bad, it’s just because of the establishment, man! – but his contribution to philosophy aside, he’s no basis for a useful approach to the work of science.

  1. In What Science Knows: And How It Knows It, a good book on the subject.
Hug an advisor today.

Hug an advisor today.

It’s inevitable.  Put two or more grad students1 in a room, and sooner or later the talk will turn to advisors;  wait a little while longer and chances are good that someone will start complaining about their advisor.  This shouldn’t be surprising.  Bosses all over are fair targets for griping, and the power imbalance inherent to the student-advisor relationship certainly doesn’t help matters2.  After being stuck in a lab together for several years, it’s a wonder that the average science department doesn’t have hallways littered with bodies.

But there’s a flip side to this, which I think might be under-appreciated:  advisors can also be awesome.  No relationship like this is going to be perfect, but a good advisor will teach you, guide you, and give you a leg up the academic ladder.  They’ll help you when you trip and faceplant, they’ll give you the advice you need (even if you don’t want to hear it), they’ll introduce you to the right people, they’ll make you better scientists.

Grad student


I’ve gotten very lucky along the way3.  Michael advised me on the undergraduate independent study that first inspired to take the idea of a research career seriously;  he also humoured me when I bit off a project that was far too much for me to chew and helped me sort through the resulting mess.  Pete, my M.Sc. advisor, got me into studying biological questions and gave me a place to work when my Ph.D. went sideways.  Luc-Alain, my Ph.D. advisor, turned me into an independent scientist and put up with far more than I had any right to ask for.  Finally, my postdoc advisor Mark has to be one of the nicest (and smartest) people that I’ve ever met and has been supportive in all the ways that have made being a postdoc enjoyable.  I’ve been privileged to work with a succession of people who’ve taught me and made me better at this science thing, and today I’d like to take a moment to be thankful for them.

Many people have poor relationships with their advisors, and there are a lot of valid questions to be asked about the grad school experience.  I don’t want to diminish the problems of anyone who has had a poor relationship with their advisor (I’ve known my fair share of bad advisors, even if I’ve been fortunate enough to avoid having them myself).  But if you have a good boss, now might be the time to take a moment and reflect on the things that they’ve done for you.  Give them a hug, a handshake, a friendly email, or a fresh data set.  And one day, when you’re in their position:  remember what it felt like to be the student.

  1. Honours students, postdocs, RAs, …
  2.  And yes, people have done research on this.  Are you surprised?
  3. Seriously lucky.  I didn’t do any of the things you’re supposed to do when picking an advisor.

Some tips for an academic job talk over Skype…

I recently had the experience of applying for a postdoctoral position at A Very Important University and made the shortlist to be interviewed.  Now, let’s face it, that’s a pretty terrifying thing to start with;  it wasn’t made better by the fact that I was doing it over Skype to a location most of the way around the world.  Visions of technical glitches, bad sound quality, and an overall horrible experience both interviewers and interviewed haunted me.  So, I spent several days polishing my talk, thinking up ways to make the Skype process smoother, and even reached out to Twitter for advice.  And boy, did I get it!  There were some great suggestions out there, a few of which really saved my bacon.  Thus, to save you the trouble of figuring all of this out for yourself, I’m going to share what I learned with you.

Your voice here: social media for academics, objections edition.

“Twitter, huh?  That’s just a bunch of people talking about what they had for lunch, right?”  *headdesk*

Hands up if you’ve heard that one.  Or any of the other clichéd objections to the use of social media by academics:

  • “I could be writing papers instead of fooling around on Twitter!”
  • “I talk to too many people already.  Why would I go looking for more?”
  • “It’s all just noise.”
  • “I don’t want to have to deal with uninformed commenters.”
  • And many, many more.

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.