Wednesday, November 28, 2012

Immortaly Tomfoolery

Their is a saying among scientists that the more you know about the scientific subject a journalist is writing about, the less of what he writes makes any sense. There is a long new article in the New York Times magazine about a hydrozoan jellyfish, Turritopsis dohrnii, which the author claims holds the key to immortality. As someone who happens to work on hydrozoans, and on aging, I can assure you that not a bit of it makes any sense. The title, "Can a Jellyfish Unlock the Secret of Immortality?" should be a dead giveaway that this is magical thinking with a whitewash of pseudoscience. The argument behind the article, striped of its misunderstandings and untruths,  goes something like this:

1. There is this jellyfish that can develop back from the medusa phase, which we normally think of as the adult, to the polpy phase, which we normally think of as the juvenile. It can then develop into the medusa phase again.
2. We are going to assume that this is the only know case of an organism that does not show a human-like pattern of aging.
3. We are going to assume that this non-human like pattern is equivalent to immortality.
4. We are going to assume that if we understood the mechanisms behind this assumed immortality, we would know how to make humans immortal.
5. We would know by now what makes them immortal except that we are going to assume that the one researcher I talked to extensively for the article who studies the species is the only one doing so.
6. We are going to assume that this one researcher is unfunded and working alone not because he is considered a crackpot, but because the rest of science is just too blind and lazy to see the importance of this man and his work.
7. We are going to assume that when he has learned a little bit more, we will achieve immortality.

I do not recommend that you read it, and mention it only because I have been asked about it, and because I would like to speak briefly about the word immortality. Immortality is defined as immunity from death. Immortal beings cannot be killed. Turritopsis dohrnii can very easily be killed. Put one out of water for a few minutes, feed it to a predatory snail, heat it, freeze it, slice, dice or frappe it, and it will be dead. Ergo not immortal. However the journalists are not to blame for the misuse of the word. A very good recent paper in PNAS from a very good careful research group is titled, "FoxO is a critical regulator of stem cell maintenance in immortal Hydra." They use the word immortal as many people in bio-gerontology do, to mean that the risk of death does not increase with age. My general impression is that using the word in this way is misleading, but that it is a lot flashier than 'nonsenescing' and therefore widely used.

Friday, November 23, 2012

Have I mentioned?

I'm now the Secretary/Treasurer of the Evolutionary Demography Society, which now exists. I'll be starting as an Assistant Professor at the University of Southern Denmark in January. We'll be moving to Odense the middle of the month. I have a terrible head cold and need to catch up on sleep. I'll soon have my first lab group that officially exists. My daughter can finally use a spoon without getting most of the food on everything but her mouth. The African violet on my desk is blooming very nicely. My cat is down to a relatively healthy weight, but I am not. I am going to sleep.

The Evolutionary Demography Society is born

We are pleased to announce the formation of the

Evolutionary Demography Society (EvoDemoS)

and to invite interested researchers to join. While many societies include life-history evolution or evolutionary demography within the range of topics they consider, no active society focuses on these topics across taxa and disciplines. EvoDemoS is intended to fill this gap.

EvoDemoS is an interdisciplinary scientific society dedicated to the study of the interactions of ecology and evolutionary biology with demography, including but not limited to patterns of mortality, reproduction and migration over age, stage and state and the evolutionary processes that produce those patterns. All taxa and methodologies are of interest. Our primary goal is to facilitate communication between researchers, and as such we are pleased to offer free membership for 2013 to any interested researcher. We invite members from students to established experts. We will organize yearly meetings to provide a specific forum for evolutionary demography. Our first meeting will be in Odense, Denmark in October of 2013, and will be open only to society members. Membership can be gained by emailing your name, preferred email address, affiliation and a sentence describing your research interests to:

Questions and comments can be addressed to this same address.

Please feel free to distribute this announcement broadly.

The Board of the Evolutionary Demography Society

James W. Vaupel, Max Planck Institute for Demographic Research and University of Southern Denmark

Vice President
Shripad Tuljapurkar (Tulja), Stanford University

Daniel A. Levitis, Max Planck Institute for Demographic Research and University of Southern Denmark

Board Members
Anne M. Bronikowksi, Iowa State University
James R. Carey, University of California, Davis
Hal Caswell, Woods Hole Oceanographic Institution
Charlotte Jessica E. Metcalf, University of Oxford
Tim Coulson, Imperial College London
Timothy Gage, State University of New York at Albany
Jean-Michel Gaillard, Université de Lyon and Centre national de la recherche scientifique
Thomas B. Kirkwood, Newcastle University
Daniel H. Nussey, University of Edinburgh
Fanie Pelletier, L'Université de Sherbrooke
Deborah Roach, University of Virginia
Rudi G.J. Westendorp, Leiden University

Wednesday, November 21, 2012


It is a real challenge to write papers that say, "here is what is wrong with this body of work I am reviewing" in a way that doesn't make the people who wrote that work feel like I am a nit-picky asshole. So I go back through my drafts multiple times, looking for things that are poorly stated or abrasive, and trying to fix them without losing the meaning. Then I send the draft to colleagues and ask them to look for anything I missed. I may still come across as a picker of nits, but I have minimized the insult as much as possible.

I am scheduled to give an interview to a radio reporter who wants comments from a not-involved scientist on a recent paper. I happen to know the senior author on that paper very slightly. In this situation I have none of the ability I would normally employ to go back and make sure the things I am saying aren't abrasive, overstated or unfounded. Rather the reporter has both the ability and the motive to find the most dramatic and controversial thing I say and put it in a context of her choosing.

Imagine that I say to the reporter, "This is really an excellent paper, that greatly increases our understanding of poodles and how fancy they are.  I'm not much of a poodle-fancier myself, and hadn't known there were so many kinds, let alone that they could do back flips so successfully. I would have worried that I would break their necks doing these experiments, but these guys clearly knew what they were doing. I may have to go out and get a couple of poodles."

The reporter could reorganize as follows: "A new study out of Paris has concluded that poodles are the fanciest dogs around. The authors compared the fanciness of a wide range of dog breeds on a variety of measures, and poodles took the cake, paws down. But not everyone in the field is fond of poodles. Dr. Daniel Levitis of Rostock, Germany is, 'not much of a poodle-fancier myself.' In fact, he says, 'I may have to go out and get a couple of poodles' What would he do with them? 'I would break their necks.'  So clearly there is still great scientific controversy regarding the worth of poodles."

I've been advised to avoid saying anything the least bit critical about the paper in question, myself, the authors or the weather, and instead to try to talk as much as possible about my own work. We'll see how that works out.

Friday, November 02, 2012

Friendly advice for writing your first grant application, actually first edition

As a first year graduate student studying birds in a university natural history museum, I largely failed to learn how to make a decent specimen out of a dead bird. While there are many reasons for my failure, including a lack of aptitude and a lack of effort, at the time it felt impossible in part because the ornithology curator who was teaching a group of us how to do it was just too good at it. She would hold up the dead bird, make a tiny incision in its belly, and then her hands would spin around it and the entire carcass of the bird would be outside of its now inverted skin, which she would hold up to show us. Then she’d grab some bits of wood and cotton, and again her hands would whirl around the bird for a few seconds, after which the bird would be right-side out and restored to a life-like shape, its feathers unruffled, its head turned to the side just so and toes overlapping, as though it was patiently listening for something. I would try to repeat this process on my assigned dead bird, would screw it up somehow, and she would come over, sigh, take the bird for a few seconds and hand it back to me, several steps ahead from where I was. Then she would say, “See?”

I never did learn, or make it in ornithology. From this I learned that of the great challenges of good teaching is that you have to know the topic well, be interested in it and have a strong aptitude for it, but you also have to be able remember what it was like to not know it at all empathize with those with less inherent aptitude.

At the time, I was also learning to write grant applications. I wrote several that first year in grad school, none of which were funded. This was partly because the ideas behind the proposal weren’t well worked out, but partly because I didn’t really know what I was doing as a grant-writer. I have now written a lot of different grant applications, lets guess 40, almost every one to a different funding source. I don’t know that I can claim to know the topic well enough to teach it, or to have a particularly strong aptitude, but I can well remember what it feels like to not know where to begin, which is a very good place to start. So with that in mind, I’m going to offer some thoughts for those trying to write their first research grant applications. I’ve recently written what I learned about applying for grants from NIH and ERC. This is going to be a lot more basic.

First, consider this picture of the time my wife turned into a giant and flattened part of southern Denmark. Pretty cool, huh? Not even Photoshopped.

Okay, now down to business.

1. Don't panic. There is a good chance it seems to you at this point like you are somehow supposed to know how grant-writing is done, and that everyone around you magically knows how to do it, but there is a good chance that no one has ever provided you with any guidance on the subject. Or at least that is where I was at when I was in your shoes. Ask for help and advice frequently. Several times during the process, have people read what you are doing so they can point out your mistakes. There is a whole culture that you haven't been initiated to, and you need a guide. The basic formula for a grant application goes like this: there is a fundamentally important question that we don't know enough about. Here is what the question is and why it is so important. Here is the piece of that question I can address, how I would address it, why that is the right way to do it, why it is feasible and why it won't fail to answer the question. Here is why I am the right person to do it. I need these resources for this part of the plan, and can't do the work without them. Reiterate the importance of the question and your future results.

2. The place to start with a grant application is to have a question you need money to answer. While that may seem horrendously obvious, I have known a fair number of graduate students who were told to apply for a certain grant, or many grants, but didn’t have a clear conception of what they needed the money for. Either the question was ill-defined (as was mine that first year) or it wasn’t really clear what the money was needed for.

3. Writing grants is a pain in the ass, and there are very few academics who wouldn’t rather be spending their time on research. We do it because we need to. That said, writing grant applications is tremendously useful to your research planning, because it gives you a hard-deadline and strict format in which you have to clearly state your research plans in a succinct and clear way. My research plans have often improved dramatically through the process of writing them into an application. Some universities require graduate students to submit a detailed research proposal before starting work on their theses. This serves the same purpose.

4. The two most common types of funding you may be applying for are for research costs and for your own stipend or salary. Small grants available to students usually focus on research costs, fellowships usually fund only stipend or salary and related costs, although some do both or are for funding travel to conferences or other specific costs. Every granting agency has rules for what each grant can or can’t be used for, and so what you apply for depends on what you need to fund.

5. There are an effectively infinite number of organizations that at least occasionally give research grants, but the chance that any one of them is the one you need to apply for is almost infinitely small. This makes finding the grants you should be applying for very difficult. The way to go about this is to avoid doing what I did. I wasted a huge amount of time online looking at listing of things I could apply for, examining the websites of various foundations, etc. Instead, ask people at your university what other students have applied for successfully. Ask faculty, other students, and the administrative staff. Most every university has people whose job it is to shepherd grant applications.

6. Whenever possible, get a copy of someone's successful grant application. Get several if you can. The instructions for every grant are different, so it is best if the application you are reading is for the same grant you are applying for. That said, there is a certain grant-like style that you will find in most applications.

7. Know your audience. Most research grants are evaluated by a small group of very busy researchers who have to get through a big pile of applications and find just a few to fund. Find out as much as you can about who these people are, and design your grant to grab their interest, and tailor it to (or slightly below) their level of knowledge of your field.

8. You need to convince them that your ideas are compelling and sound, your goals achievable and the whole thing in line with the purpose for which the grant is given. You also need to convince them that you are the person to do it. Doing all of this is harder in less space than in more. When you only have a page or two, as is often the case with the grants available to students, you can't get bogged down in the details. Your writing needs to be crisp and to the point. I often write much more than I need and then edit it down repeatedly. No matter how much time you put into writing a section, if you find it isn't necessary, cut it.

9. Beware of giving too much methodological detail. The committee reviewing the grants generally won't care what concentration your solution will be at, where you will order the food pellets or what software package you will use to analyze your data. That said, if one of those details is key to understanding what you plan to do, of course you need to include it.

10. Try to write it long enough in advance that you can set it aside and come back to it a few days later, perhaps more than once. Once you've worked it over more than a few times, you need some time away from it before you can really see it again. Very good writers can produce very bad writing when they've lost their ability to take a step back and just read.

That's my ten cents (inflation). I'm sure there are things I've missed, but those are the main lessons that I can remember learning. Good luck. Now quit browsing the internet and get back to writing.

Genus species

When writing the genus and species of an organism, the genus name is capitalized, but the species name is not. Also note that both are usually italicized to differentiate them from common names.

Right: Homo sapiens
Wrong: Homo Sapiens, homo sapiens, Homo sapiens

This is a long established rule that is consistently followed by scientists but generally ignored by many science reporters and other non-scientists. It becomes very useful when taxonomic level could be unclear.

For example, the extant members of Bison are bison (the American bison) and bonasus (the European bison, or wisent). While bison has been out of immediate risk of extinction for some decades, bonasus populations remain small and have started to rise only recently in captivity and intensely managed reserves. Commercially available bison meat is bison. It is more commonly sold as buffalo meat, although the term buffalo is more properly used for Syncerus and Bubalus, rather than Bison.

It is prefered, but not in all contexts, that in scientific writing one put the abbriviated genus name ahead of the species name. This is done in part because many genera have identically named species. For example, Dendrocopos major, Parus caeruleus and Parus major are all birds of Europe. While P. major is clearly in Parus, P. caeruleus is sometimes placed in Cyanistes.

Thursday, November 01, 2012

Thank a meteorologist

Where I live, or rather in several of the places where I have lived, meteorology often seems to have about as much predictive accuracy as astrology. The German weather website predicts rain for Rostock all afternoon and evening, starting 2 hours from now, while predicts no precipitation at all today. It is currently raining.

Because this kind of obvious failure of retail meteorology is so common, bashing ‘the weatherman’ is a popular and easy past time, and I think this shapes the views of many people on meteorology generally. But when things like Hurricane Sandy do things like this to a densely populated portion of a continent and kill only dozens of people, rather than tens of thousands, that is because of the very healthy state of meteorological science.
Imagine, if you will, the impact of Sandy on the U.S. if meteorology hadn’t progressed in the last hundred years. We would have gotten reports of a hurricane hitting Jamaica, Hispaniola and then Cuba. Folks in New Orleans, hit by Katrina a few years earlier, with even less warning than in the real world, would start evacuating, along with much of Florida and the Gulf Coast. No telling where this thing might hit. New Jersey and New York would scarcely take notice. When Sandy clobbered the Bahamas, people in the Carolinas would need to evacuate fast. Who knows who the monster is coming for? Two days later when the surf in New Jersey started getting really rough, and the wind really strong, the idea that New Jersey and New York could get hit would occur to a lot of people. But what does it mean to get hit? Lots of rain and wind? Flash floods? Would anyone have guessed that there would be a nearly 14 foot storm surge in New York City, flooding houses, lobbies and subway tunnels with seawater? Would lower Manhattan have been evacuated at all? Would there have been time to get out? I doubt it.

My guess is the East Coast would have been far less prepared than New Orleans was for Katrina, because people in real world New Orleans, even if their government let them down, could turn on the TV and know what was coming. In a meteorology-free New York, the idea of large parts of the city being underwater would have seemed ridiculous until walls of water were ripping through tunnels still full of people.
We have come to take for granted that we should be warned, accurately, of major weather events days in advance, and we grumble about the uncertainties and inaccuracies. There is certainly still room for improvement. But the fact that New Jersey was named as one likely landfall while the center of the storm was not yet to Cuba is absolutely amazing. That requires a level of understanding and predictive computing that I find hard to fathom. It frankly seems a bit like magic. The National Hurricane Center nailed this one, and in so doing prevented tens of billions of dollars in damages and tens of thousands of lives. Somebody deserves a medal. Thank you meteorology.