Wednesday, December 19, 2012

Unboiling letters of recommendation

Laboratory work, especially demographic laboratory work, is labor intensive. (Perhaps that is why it is called a laboratory?) I couldn't do the experiments I do without lots of reliable helpers. At the Institute where I work, and at most universities I've seen, much of this labor comes from eager young undergraduate students. They work hard (if carefully chosen), want to learn and don't cost a great deal.

This is the last week I will employ most of my wonderful mob of students, and so today I am writing letters of recommendation for almost all of them. I've gotten to know most of them quite well, and I like all of them, so it shouldn't be such a hard task. But of course I have found a way to make it hard. I feel I owe it to them to write a memorable individual letter for each person, not a formulaic boilerplate with a few details changed. And while their personalities are very different, many of the positive things I can say about them in these letters are all the same, leading to boilerplatedness. I suppose the need for creativity within constraints such as these should be taken as an artistic challenge.

Wednesday, December 12, 2012

Unbe-fricken-lievable incom-shitforbrains-petence

So we just, finally, got the re-typeset copy of our previously mangled article back. The good news is that relatively few modifications were made this time. The bad news is that the production editor sent  the wrong version of the paper for typesetting. This is the draft we sent them last summer, rather than the up-to-date version from this fall. Where the hell did they find this guy?

Friday, December 07, 2012

Traditionally successful

I have had a hand in advising several doctoral students, but none of them have been my student in the sense that I am their major professor (what the Germans would call Doctorvater*) because I have not been a professor. Starting in January I will be an assistant professor, and starting in February I will have my first for-realsies doctoral student. She and I have already worked together for some years, and written papers together, and I am confident that she will be wonderfully successful.

That said, it would be irresponsible of me not to think through what barriers could arise that would potentially threaten the successful completion of her doctoral work. Of course there are all sorts of logistical and scientific questions to consider in designing her research, to make sure it will produce something that will be publishable and launch her on a successful career. But I have known enough doctoral students who stopped before getting a doctorate that I feel like I have a fair sense of what goes wrong, and the scientific difficulties (e.g., almost getting killed in Papua New Guinea) tend to cause delays, rather than make people stop altogether. I have not known any doctoral students who failed, in the sense that they produced dissertations that were simply indefensible. I have known many who didn't produce a dissertation or receive a PhD.

These nondissertators were in my experience no less bright, driven or well resourced than other doctoral students. Some of them suffered from health problems, scientific set-backs or family emergencies that exacerbated their situations. But the characteristic that unites them is that they were poorly matched with their Doctorvaters or Doctormutters. Sometimes it was a simple personality conflict, but more often the mismatch was in terms of the advising style and the need for advice. Students who need guidance and aid often end up with ultra-busy hands-off advisers. Students who need to be left alone to do what they already know how to do sometimes end up with micromanagers. I spent a fair bit of time as a doctoral student thrashing around, not getting as much advise as I needed, not even knowing what the rules of the university were. A good friend in another lab wasted a lot of time fighting with her adviser whose overzealous attempts to advise were often an impediment. Both of us at times considered dropping out, transferring to other labs, or committing felonies, but a combination of luck, pigheadedness and good burritos got us through. We had several peers who took other paths in response to adviser mismatch. It is a very rare student who will go to her adviser and say, "I want you to alter your approach to advising," and not all advisers would respond positively. I hope that my student will say this to me if necessary, and knowing her, I think she will. If she doesn't, I'll ask.

In the academic world, leaving the academic world is generally thought of, and often spoken of, as failing. If you are in a doctoral program and leave without your doctoral degree you fail. If you get your doctorate and then make a career in academia, you succeed. What I have done is clearly success, so to do otherwise is clearly failure. This is of course a definition born of bias and self-congratulation. My job as a Doctorfater is to simultaneously help my student to succeed in the traditional sense and to make it clear that other paths are not necessarily failures. Producing a garbage dissertation is failure. Finding an alternate route to a happy productive life is not. I hope that making this clear will help my student succeed, in the traditional sense.
*Vater in German is pronounced like 'Fah-tar' in English and means father. It has only just now occurred to me that Darth Vader's name was rather a large hint.

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.

Monday, October 22, 2012


I love Italy. Friendly people, good food, great art, nice weather, etc. But there is something in Italian governance traditions that make me feel okay about not living there. Prime examples are Berlusconi and this, the conviction of six seismologists and a government functionary for failing to predict an earthquake in L'Aquila that killed 309 people in 2009. More exactly, they issued a report that said that it wasn't possible to predict whether or not their would be a major earthquake that year, but estimated the probability as fairly low. The earthquake came, and they are the scapegoats.

Imagine if you will that an Italian man goes to the doctor, and asks if he is going to have a stroke that year. The doctor gives him an exam, some blood tests and a questionnaire, then uses the best available methods to estimate that this man has only a 10% chance of having a heart attack that year. The man goes for a hike, has a heart attack, dies. Should the doctor go to jail for failing to know for sure that the heart attack is coming? Of course not. We don't put people in jail for failing to know things that no one could possibly know. We don't, but apparently the Italian courts do.

Now imagine the Italian government comes to you next week and wants you to produce an expert report on an unpredictable topic for them. Would you be eager to help?

Tuesday, October 16, 2012

Friendly advice for your first grant application, ERC edition

Earlier this year I wrote a fairly long post about the experience and lessons of completing my first NIH grant application (nightmare). While I still haven't heard back if NIH are going to fund me, the good news is that my application has been deemed to at least have the scientific merit for funding (the scientific review board ranked it ahead of almost all of the other applications). Now they have to decide if it makes sense for them administratively to fund it. I should hear some time this month, I hope.

In the mean time I've been applying for more grants (three applications I'm involved in have been submitted in the last three weeks), because what else is there for scientists to do? I've just completed my first grant application to the European Research Council (ERC). I've heard from several people that my NIH post was helpful, so I'm going to offer a few of my thoughts on the ERC process.

Before we start, think about how cool nature is. For example, consider this American Dipper my wife and I saw in Lassen Volcanic National Park a few years ago.
Now, with that in mind:

1. Don't panic.  The ERC process is far less brutal and inhuman than NIH's. Where NIH's instruction booklet is 264 pages and requires numerous supplementary online documents, ERC's is 77 (really only one 40 page section of it was necessary for me, and it is well organized) and requires very little outside information. It took me far less time to complete the ERC Starting grant application than just to figure out how one in theory applies for an NIH grant, despite the fact that I was applying for eight times as much money from ERC, and the funding rate is somewhat better. The whole ERC process, including a lot of reading relevant literature I wasn't previously aware of, took me about three weeks of very hard work. There is a reason so many American academics are in Europe these days. There is no industry of writing ERC grantsmanship advice the way their is for NIH because it just isn't necessary. That said, I'll offer a few bits that may be helpful.

2. The type of grant I applied for, the ERC Starting Grant, is the one most people applying for the first time will apply for. "Starting" in this case means early in your career (at least two and no more than I think seven years since you got your PhD) rather than necessarily your first grant. They also have other grants for people later in their careers. The idea is that a promising early-career scientist applies for money to start a research group at a European university (or other academic host, like a Max Planck Institute). The host is named in the grant and has to provide a letter promising to employ the applicant for at least the duration of the grant (up to 5 years) if that application is funded. It has often been the case that applicants would apply with one host and then upon getting funded used that wad of cash an enticement to get hired somewhere else, but I hear that the ERC is trying to clamp down on that. They retain the right to tell you that you can't take it with you.

2. Try very hard to get a copy of a successful ERC application, the more recent and the closer to your field, the better. While the instructions are pretty clearly written, it is always helpful to look at how a successful application is organized. That said, make sure you follow the latest version of the instruction. A friend of mine who is also applying for an ERC this year thought he was supposed to use the 2012 instructions, because it is 2012. Silly friend! If you write your application in 2012, your application will be reviewed in 2013, so use the 2013 instructions. They don't seem to change too drastically from year to year, but they do change.

3. Be aware that when they say you have to have your PhD for at least 2 years, they mean the date physically written on your diploma has to be at least two years before they publish that year's call for applications. I wasn't eligible to apply last year because while I finished my PhD more than two years before the deadline, the somewhat later date written on my diploma was less than two years before the somewhat earlier date when the call for applications was published. They don't care about your citizenship or residency, but they do care what date is written on your diploma.

4. They review in two rounds. The first time they look at your CV and publications and a five page project description called an 'Extended Synopsis.' (Sort of like an unabridged compact edition). If you make it through the first round, they look instead at a 15 page scientific project description that includes more detail, a methods section and your proposed budget. The five pager really is a compact version of the 15 pager minus the budget, and there is no reason you can't copy and paste almost all of your text from the first into the second.

5. ERC has a list of 25 topic-specific evaluation panels that review these applications. Before you start writing, decide which panel you are aiming it at. When they publish the names of the panel chairs, be sure to look at the recent publications of your panel's chair so you know your audience.

6. You will need the help of an administrator at your proposed host. Find out who that person is and give her at least a month notice that you are applying. Chocolate is not a bad idea.

7. Oh yes, one last thing. The amount of money you can ask for doesn't depend on which country your host is in, but what you can do with that money does. My proposed host is in Denmark, which means I can hire about one third the number of people that I could in Germany with the same budget, and perhaps one tenth as many as in the least expensive EU countries. But apparently they are so focused on the scientific merit of the project and applicant (and to a lesser extent the host) that which country you propose to work in or how relatively expensive it is isn't a big concern for them.

That's about it. The three weeks I gave myself to get this done was clearly too little time, and I'm now exhausted and behind on everything else. My application probably could have used another couple of days of polishing and reading through by friends. But all in all I think the ERC process is quite reasonable.

Good luck and happy grant writing. I'm going to try to remember what papers I was working on before I started writing grants again.

Monday, October 15, 2012

In which I use some strong words on the topic of a botched editing job

So this big long review article my collaborators and I sent to a very good scientific journal was sent for one last copy-edit before it was published. This is normal, most journals have a copy editor look things over right before typesetting. This particular paper had already been professionally copy edited, but hey, there is always room for improvement. So we get back the typeset version from the production editor (who works for the corporate publisher of the journal and is in charge of turning the accepted paper into a formatted, typeset publication), and an hour later, we get an email from the scientific editor (who is a scientist in charge of deciding what gets published and makes decisions about scientific content) that the copy editor (who works for the production editor and is only supposed to correct grammar, punctuation and such) is an "aggressive copy editor" and we should check the paper carefully. So we sit down to read through the paper and figure out what this means when HOLY SHIT! I notice that the very first sentence of our paper directly contradict the rest of its content. And then YOU ARE FUCKING KIDDING ME?! I notice that my coauthor's name is spelled wrong. Then LET LOOSE THE DOGS OF WAR! I see that the very central sentence of the paper, the one that defines the really important concept that we are introducing and talking about, no longer means anything at all. And then, ARE YOU TRYING TO KILL ME?! I see that a paper written by a very senior colleague who I've only slightly corresponded with is now attributed to me, as though I wrote it. To top it off ARE YOU SOME KIND OF IDIOT?! there are now all sorts of punctuation errors, formatting errors, random characters inserted in the middles of words. So I think maybe that's the worst of it, and then HOW HAVE YOU NOT BEEN FIRED YET?! I figure out that the copy editor went through and sorta tried to rewrite the paper, adding a sentence here, taking out a clause there, HOW IS THIS POSSIBLE inserting parenthetical phrases with no closed parenthesis. (I DON'T UNDERSTAND! Oh, and MAKE IT STOP! the names of the demographic phenomena have been changed to something the copy editor thought sounded nicer.
So we figure maybe the copy editor was high on crack, and we write to the production editor, whose job it is to make sure the copy editing was done right, and we politely explain the problem, and ask that we would like to make sure that we don't miss any errors that may have been introduced, and so could we please have the list that he has of the changes that were made, and he SATAN! SATAN! writes back a one sentence email telling us we just need to follow the instructions he already sent. Considering I spent more than a year in total working on this paper, I think I am handling it rather well. DOOM! DOOM!

I have now written a somewhat less polite email to the production editor demanding that the pre-vandalized version be used, as we can't possibly find and mark all of the hundreds of places where the paper was damaged. My hope is to end up working with a different production editor, one who is not so BLATTANTLY STUPID unconcerned about the quality of the product.

Wednesday, August 29, 2012

When animals aren't 'animals.'

I know a guy who has fishing licenses in about ten states. He doesn't fish, but he does study salamanders, and according to the fishing regulations in many states, salamanders are fish and you need a fishing license to mess with them. Salamanders are of course not fish, unless you are a hard-core cladist who thinks that all vertebrates are fish. State fishing officials are not generally hard-core cladists, just people who write and enforce regulations and don’t really care if salamanders aren’t fish.
A similar situation arises when it comes to laws governing ethical animal research. If a scientist wants to passively observe a bunch of animals in the wild, she needs to go through all kinds of ethics boards and paper-work to make sure she is complying with these laws. If another scientist wants to slowly dissolve a bunch of live insects in acid, he just needs to buy some acid, because legally, invertebrate animals aren’t ‘animals.’ Animal ethics laws generally don’t apply to them. I say generally because their are particular exceptions. Switzerland and Norway consider lobsters and their relatives to be animals, so you can’t just drop them in boiling water (at least not in a scientific context), you have to kill them humanely. England extends animal protection laws to the Common Octopus, but apparently not to other less common octopuses, so it pays to be common.

For a researcher like myself, who studies invertebrates in the lab, this is a very convenient absurdity. It means that when I want to feed live brine-shrimp to my hydra, I don’t have to ask any committees to review whether the feeding is humane to the brine-shrimp or the hydra. I don’t need to get official approval for the size of container I keep barnacles in.
I approve of laws, regulations, forms and committees that require the ethical treatment of animals in research, and I try hard to follow the principles they are intended to enforce. I am also very glad I don’t personally have to deal with the red tape.

Tuesday, August 21, 2012

Letter to the Committee on Science

Dear Committee on Science, Space and Technology,

I would like to offer you my perspective as an American scientist currently working oversees. I work with scientists from all over the world, and frequently encounter the stereotype that Americans are willfully ignorant and prone to rejecting established scientific facts. Efforts to argue against this view are made nearly impossible by the frequent counter-factual statements made by America's political leaders, including those whose jobs specifically call for some understanding of science, such as those on science committees. While Rep. Akin has shown himself to be a particularly questionable choice, his membership demonstrates that no particular knowledge or understanding of science is expected of committee members. Indeed, it would appear that a significant number of committee members have repeatedly demonstrated a strong antipathy towards science.

This is an embarrassment for our great nation, and tarnishes the reputation of American science and education. I would like to suggest that our political leaders in general, but members of science-focused committees in specific, harm the USA when intentionally ignoring, misunderstanding or inventing scientific facts. This is because good policy can't be based on false knowledge, but also because our country is made to look like a bunch of fools. As such, I would suggest that some knowledge of science should be a prerequisite for membership in a science committee. The dim view that many in America and around the world currently take of your committee could perhaps be improved by removing one of your most glaringly ignorant members.

Dan Levitis

Friday, June 22, 2012

See no seagull

One advantage to living in the tallest building in town is that we can see who's sneaking around on the roofs of other buildings. That is in fact part of why our building was built so tall. Back when this was the German Democratic Republic (East Germany), this building was occupied mostly by the  Stasi (secret police) whose job it was to keep an eye on everyone all the time and their families. 

The building next to ours was the Stasi office building for the state. It has not only been taken over for university use, but there are Herring Gulls nesting on its roof. I spotted two big chicks wandering around yesterday. It is a great place for nesting: high up, with a rim so the chicks won't jump out, and fitted with the finest 1970's surveillance equipment. The roof is even roughly chick-colored, which is probably why until now I have seen no seagull.

Thursday, June 21, 2012


15C (59F) is quite cool for summer in New York and a normal summer day in Rostock.

25C (77F) is a normal summer day in New York, and a really hot day in Rostock.

35C (95F) is a really hot day in New York, and hotter than it has ever been measured in Rostock.

45C (113F) is hotter than it has ever been measured in New York and would kill half of Rostock.

As I pack for a trip, I am forced to wonder not only what the weather will be like in New York, but if 35C in  New York means the same thing to me now that I have been living in Rostock.

Tuesday, June 19, 2012

Field specific meanings

In demography, the phrase "historical demography" means studying the population processes of human populations of which we have historical records. In population genetics and other subfields of biology, it means trying to estimate past changes in population sizes based on the genetic patterns of current populations.

In demography, fecundity means capacity to produce babies and fertility means realized production of babies. In biology, these meanings are reversed.

In demography, EPC means European Population Conference, the largest yearly demography meeting in Europe. In biology, EPC means Extra-Pair Copulation.

Friday, June 15, 2012

Some people

So I was kvetching to a friend the other day, pointing out that I could make far more money and work fewer houes with less training and more job security in a country and state of my choice as a high-school biology teacher, when she was so rude as to ask me why I didn't do so. As though that was a realistic option!

Wednesday, June 13, 2012

Brusca and Brusca

My family is genetically Jewish and exercise the occasional fancy that we are in some important way culturally Jewish as well. We like bagels and go to relatives' houses for Matzo Ball Soup on Passover. We didn't have bar and bat mitzvohs or learn any Hebrew, but we learned enough Yiddish to insult each other and had large 13th birthday parties. When my 13th birthday party was approaching, people started asking my parents what they should get me, and my parents started asking me. I already had most every material object I wanted, and so I told them I wanted books about animals. I had decided several years earlier that I was going to be a zoologist, and I thought it would be nice to have some grown-up books about zoology. Well little did I know that I was going to get books like this:

Invertebrates, but Brusca and Brusca. And not the Second Edition (2003) with the nice color photos. Oh no, this was line drawings and black and white plates of everything from ciliates and amoebae to sea-squirts and squid. This was lists of the sub-classes within the classes within the sub-phyla within each Phylum. This was extended discussion of the bauplan concept, and pre-molecular phylogenetics. This was 1990.

I was simultaneously thrilled and offended. Why would anyone give a book like this to a 13 year old? Ridiculous! How could tardigrades possibly survive exposure to raw vacuum? Ridiculous!

Someone (I'm sure it came with a card, but I have no memory of who gave it to me.) had spent a fair chunk of money to give me a book that is really intended as a reference for invertebrate zoologists.

Now, let's skip forward 22 years and a few weeks, and we find me at my desk reading the Brusca and Brusca chapter on Phylum Porifera (sponges) as I prepare to write the outlines of a research proposal focusing on this group that I have no knowledge of. Of course the taxonomy has been changed 22 times since then as more and more molecular data have become available, but mostly it has changed back and forth, so Brusca and Brusca are still pretty much right. Most of the rest of the detail they give is still approximately true, and despite being a formulaic listing of facts, the writing is not too painful. Really very useful.

So whoever gave me the book, you probably never got a thank you card, and you probably don't read my blog, but thank you. This is turning out to be one of the most useful presents I've ever gotten.

Monday, June 11, 2012


When colleagues started telling me that what I was doing was brave, I knew I was in trouble. People tell you are brave as you march off to war, or volunteer to babysit multiple toddlers around bedtime, or (it seems), when you undertake the organizing of a new scientific society. They mean, "Man, you're going to end up unemployed, but I'm sure glad you are doing it instead of me."

I waited until they had a few drinks in them and had mostly finished going back for seconds on the salmon, then commandeered one of the cocktail tables as a podium. I proposed the formation of an society and then opened the floor for discussion.

The good news is that we now have about 50 members including many of the big names in the field. The bad news is that everyone seems to think I have an actual plan. How will we fund the first meeting? What kind of official and financial structure should we have? Will we take over that other, mostly defunct but somewhat related society for the benefit of their infrastructure and their resources, or will we start fresh? Do we need to incorporate? I don't know any of these things.

So here is what I am doing. I'm organizing the election of a board, and I'm making sure there are people who know what they are doing standing for election. I'm communicating with the people who will organize the first meeting next year. I want the society to exist, and I'm happy to help, but I certainly don't plan to run the thing by myself. That would be a little bit too brave.

Sleeze of sponges

The term of venery for sponges: a sleeze.

Example: The vessel must have rested there many years, as it was more than half covered in a sleeze of the most enormous sponges.

The dangers of autocorrect

I sat down to write a quick email at a computer I don't usually use. Autocorrect was not turned off because I don't usually use that computer. In an email to a senior colleague I tried to write, "I completely understand" but got out "I  completely undrestand." Autocorrect changed it to, "I am completely undressed." I am happy that I proofread my emails.

Thursday, April 19, 2012

Egg-maculate conception

I've long said that if I was a benevolent deity the first thing I would do was give penguins the ability to produce live offspring at sea, the way whales and otters do.  My opinion has been that all birds lay eggs that need to be kept warm and be exposed to air, and no bird can give live birth, and therefore it would require the intercession of a god to produce a bird that could develop its eggs either internally or under (cold) water.

Well, that may still be true, but consider the following  from the BBC today:

'Eggless' chick laid by hen in Sri Lanka 

Instead of passing out of the hen's body and being incubated outside, the egg was incubated in the hen for 21 days and then hatched inside the hen.
The chick is fully formed and healthy, although the mother has died.
Let's assume for a moment that this is true, and neither a prank nor a misunderstanding. What seems to have happened is that the egg was retained inside the mother's reproductive tract. This (technically called dystocia) happens occasionally, especially to older hens. The egg just gets stuck, and usually eventually breaks and comes out in pieces, which can often kill the mother, and which also smells terrible, as the egg is usually quite rotten. But in this case it appears that the retained egg developed successfully, and the mother wasn't killed until the chick was viable. So assuming this is true, it is the first example of live birth in a bird I can find.

Now before all you penguins trade in your carefully maintained rock scrapes and hole-nests for shrines to the fertility god, keep in mind the following:
1. The mother died, probably quite painfully, and therefore is not around to feed the chick.
2. It would be hard for a trait like that to spread through a population, as each mother could produce only one offspring, and sexually reproducing mothers need to produce at least two adult offspring to reach replacement.
3. It probably isn't true anyway.

Still, it is an interesting story. If a group of birds could for some other reason first evolve to have un-calcified eggs, then it seems more likely that live birth would have a chance of evolving.

Tuesday, April 03, 2012

Accepted, but...

We have set ourselves a difficult task. Some months ago, my friends and I submitted a review article, clarifying some common (within the scientific literature) misconceptions, to a very good anthropology journal. Today we heard back from them. The editor explained that it took longer than usual because he had sent it out to "several" reviewers, and then "several more" and was waiting to get comments from all of them.

The good news is that all the reviewers seemed to like it, and the editor knows which issue of the journal he wants to put it in, which we take as the paper being accepted. The bad news (or at least time-consuming news) is that all of the several and several reviewers made long lists of things they would like to see changed, added, clarified or reorganized. I have not yet finished reading all these comments, but I don't see a lot of repetition, meaning that we have hundreds of distinct comments and criticisms to deal with. In the months we were waiting, we also showed the draft to a couple of colleagues, who gave us still different but also very useful comments. The good news is that the editor has given us permission to go well beyond the usual page limit for this journal in order to deal with all the reviewer comments. The bad news is that we now can't use space limitations as an excuse for not dealing with relevant points or citing relevant literature. So we have a great deal of rewriting to do.

Part of the problem with writing an article pointing out places where other people's thinking or language has been unclear is that one has to live up to very high standards for clarity in one's thinking and language. We've already extensively rewritten this paper a few times, and each time it has gotten clearer. Nevertheless, a large portion of the reviewers' comments are right on, and further clarification is needed. By the time this thing comes out it will either be brilliant or a total muddle. I'm not clear which.

Thursday, March 22, 2012

Conference Spam

I get several emails a week like this:

The organizing committee is pleased to announce that the 2nd Annual World Congress of Nano-S&T (Nano S&T-2012), which will be held from October 26 to 28, 2012 in Qingdao, China. The congress will consist of 12 streamlines covering topics including: Nanosciences and Technologies, Nanomaterials, Analytical tools for Nanotech, Nano-electronics, Nano IT, Nanocoating, etc. This conference will bring together over 1000 experts and specialists from all over the world.

Based upon your contribution to the field of Nanotechnology, we invite you to give an oral presentation at Section 4-4: Etching Process about your recent work. Certainly, you can look through the program and select a session at your priority. We will be honored if you can deliver a speech during this event. Your involvement in this congress will be invaluable for the development of the program.

The full program with speakers’ profile and presentation’s titles will be released at the conference website in a few weeks so that you can know what specific subjects will be covered by the other speakers. You may log on:

I am pleased to send you a conference brochure about Nano-S&T2011 in the attachment.

We would be honored if you could attend the Nano S&T-2012 Conference.

I will appreciate it if you could forward this invitation letter to the experts who may be interested in us.

Sincerely yours,

Ms. Selina
Most of the "congresses" are in China or India and they are all on topics that have are totally unrelated to my work. I think most but not all of these conferences are intended as actual events, but the point of all of them is to collect registration fees.

Friday, March 16, 2012


Hungry buzz heralds spring
Watchful grin, floating. Smack
Bloody bugs

Wednesday, March 14, 2012

Friendly advice for your first NIH grant application

I've just submitted my first National Institutes of Health grant application (or rather administrators at my collaborator's university have submitted an application that I wrote most of). In preparing to write it, I read a lot of online advice ranging from the general 'how to write an NIH grant' to the specific 'the clause-structure I use while writing my cover letter for maximizing the chances that it will be sent to my preferred review committee.' People who regularly apply for NIH money refer to NIH funded research as an industry, and like any industry, there is a lot to know to compete successfully. NIH pays or invites some people to write advice on 'good grantsmanship' and many others, for a variety of reasons (perhaps on their blogs) write advice essays. Most of this advice starts with a paragraph or two along the lines of, "I've been conducting NIH funded research since 1982, and am currently involved in seven NIH funded projects, four as PI (Primary Investigator). I've served on 12 review panels and helped to amend the rules on permissible administrative expenditures on research grants in 2002 and again in 2006." And so on. The message is, "I am an expert on NIH funding applications and therefore qualified to advise you." While these people certainly are qualified and anyone planning to apply should read as much of their advice as bearable, there are two points I would like to make about this that they may not have considered. The first is that the way they write their advice, including the way they lay out their qualifications, reads very much like an NIH application. It makes me wonder if becoming expert in these applications makes it hard to write a love letter that isn't in the form of a funding application."Specific Aim 2: Produce a rapid natural release of endorphins, aiding current pleasure, speeding forgetfulness of discomfort and fomenting pair-bonding."

Second, and more seriously, I have the impression that none of these people nor the people writing the instruction books or the FAQs on the NIH websites have any memory of what it is like to not already know how to apply for NIH funding. The instruction book is full of rules that are explained not in terms of what you have to do, but in terms of how what you have to do is different than what it was before the changes to regulation #SF5326BB777. They use all sorts of words that are normal English words but don't mean what they normally mean, without explaining, because however NIH usually uses a word is its normal meaning to them. (This, by the way, is very close to the technical definition of jargon).

So I'd like to offer a few pieces of advice to people considering applying for their first NIH grant. I am not an expert, have never served on (or been invited to serve on) a review panel and may or may not ever have any NIH funding, but when I was a kid my dad worked just a few blocks from NIH headquarters, and I once spilled an incredibly powerful neurotoxin on myself inside an NIH laboratory. Before I start, consider this unrelated photo (of a 2.5 inch long weevil I once found in my hair) that helps to break up the text:

Notice that its sharp mouth parts are at the end of its huge nose. Cool huh?

Okay, here goes:

1. Before doing anything else, ask yourself if you can spare the two or three hundred working hours your first NIH application is likely to take you. If you can't, don't. Subsequent applications may take an order of magnitude less time, but this is going to be a slog.

2. Before doing anything second else, find colleagues who know all about applying for NIH grants and buy them beer, chocolate, whatever it takes. Wash their cars, baby-sit their kids, fix their refrigerators, do their laundry. This will save you so much time. If you are very lucky your department/institute/whatever may even have someone whose job includes guiding you through the process. If so, flowers and a gift-certificate to a nearby spa are in order. If you can by any means obtain copies of past successful grants to use as Rosetta Stones in figuring out what the instructions mean, then you have some chance of retaining your sanity.

3. Next, find out who is your SO (Signing Officer, an administrator officially authorized to sign legal documents on behalf of your organization). You don't submit the grant, the SO does. She also has to do various other registration tasks, meaning that they need to know that you will apply several weeks before you actually do. If you just found out that the deadline is in three weeks, relax. There will be another deadline some months in the future, and by then you may have found some other way to fund your work. The SO will need all the forms you are to prepare at least a week before the official due date, as there are a whole bunch of other forms they have to fill out seperately.

4. Don't panic. Download the 264 page instruction book (a.k.a. "SF424 (R&R)
Application Guide for NIH and Other PHS Agencies"). Here is a picture of a moorhen to help you not panic as you download:

Can you see how long its toes are? Fricken' long. Imagine soaking your extra-long toes in a nice summer pond.

5. Do not print out the instruction book. It is 264 pages. You will need to constantly jump from section to section to hunt down the clues and riddles needed to fill out each of the approximately 30 forms you will complete. Keep it digital so you can search for relevant terms.

6. Do print out this glossary of NIH terms. Then read it. Then read it again to see if you understand it any better. Keep in mind that while necessary, this glossary is wildly incomplete, because NIH people can't guess what terms non-NIH people won't understand. Also keep in mind that when they use a term to define itself, they mean well.

7. The National Institutes of Health are called "Institutes" because they have quite a few different topic-specific Institutes, plus a bunch of Centers and several Divisions. You are supposed to know which of these is most likely to be interested in funding your work, contact the appropriate PO (program officer) and pitch it to them before then writing in your cover letter than you contacted that PO and she encouraged you to apply to that Institute, Center or Division. There are very detailed guidelines you should follow in writing to that PO. You are supposed to already know which PO within the appropriate branch is the appropriate PO. The only way I found of finding this out was to spend countless hours on the NIH web pages learning about the structure of NIH, then countless more hours reading those pages before making a wild (and wrong) guess. Luckily the person I wrote to (who wasn't even at the Institute I thought she was at) directed me to another person, who told me that I was heading the wrong way. Eventually I made a decision.

8. Go through the instruction book and make a list of all the forms and attachments you will need. Depending on the specifics, there could be anywhere from 15 to infinity of them. On your list, make notes as to the purpose of each form and what is an attachment to which extension to which sub-form. Also note which parts you have to do and which parts the SO has to do, and then confirm this with the SO. Then look at these pieces in the pile of example applications you've gathered.

9. Don't plan any vacations for before the due date. Plan a vacation for after the due date.

10. You may notice that I have not yet mentioned anything about science. At least once a week, think about the scientific goal of your application. It is very easy to lose track of the fact that there is some reason you are putting yourself through this.

Monday, March 12, 2012

Evolutionary biology vs. evolved biology

Once, during a medical exam, the doctor asked me what I did. I said I was an evolutionary biologist, to which he replied, "oh, so not a creation biologist?" His tone of voice made it clear he thought it was funny that I had to specify evolutionary, as though a biologist in Berkeley could possibly not believe in evolution. Considering where his hands were at the time, I didn't stop to explain to him what the term "evolutionary biologist" means. Every biologist knows, or should, that Theodosius Dobzhansky wrote, "Nothing in biology makes sense except in the light of evolution." The vast majority of biologists, of all disciplines not only know about evolution, but accept it as a necessary part of any complete explanation for the things they study. But a large portion of biologists don't regularly think about evolution; it is not the part of the explanation they are interested in. A large (and I think increasing) proportion of biologists study the interactions of atoms, molecules, organelles, genes, cells, etc. And while they may connect their work to evolution in some way, they are not basically asking questions about evolution, but about the details of the proximate mechanisms which make organisms work. That these mechanisms are the result of evolution is often not particularly relevant to the present question.

An example: A couple of years ago I attended a workshop on bioinformatics in aging research. There was a dinner the night before the talks started, and the bioinformaticist organizing the workshop asked me about my training and research. I said, "well I study the evolution of demographic patterns, particularly how constraints on natural selection lead observed demographic patterns to differ from the predictions of evolutionary theory." He replied, "Oh, but you are also trained in biology?" What he meant by this, I discovered, was that I also had some training in the molecular nuts and bolts that to him are biology. Evolution is a process that shapes biology, but in his view, and I think the view of many of the people there, does not in itself count as biology. Asking him if he ever incorporated evolution into his work, he explained that he had, comparing how networks of gene interactions differed between fruit fly and nematode. Fair enough, comparative biology is surely the study of evolution, but his approach to it required no technique or concept from evolutionary theory. He produces good and useful science, and gives no more daily thought to evolution than I give to promoter regions. I am certain that he would not be offended to be described as a good biologist who believes in evolution, but is not an evolutionary biologist.

A definition from wikipedia: "Evolutionary biology is a sub-field of biology concerned with the study of the evolutionary processes that have given rise to the diversity of life." This is somewhat too narrow in my view, but it is close enough given that it is past my bedtime.

This has all come to mind because of the post I wrote yesterday, about weeds evolving resistance to Monsanto's best-selling herbicide, and the failure of Monsanto's biologists to predict this. A good friend of mine, who is deeply knowledgeable about matters environmental and agricultural, responded by asking how Monsanto's biologists could have failed to predict the apparently obvious facts I was pointing out unless they were A, Tools; B, Fools; or C, having their results manipulated by suits. This is a reasonable and interesting question, and I'll venture an answer. My guess is that they were neither A nor B, and that C went on but was not a major factor. Monsanto did have an enormous financial stake in convincing regulators that weeds would not evolve resistance to Roundup, but they also had an enormous stake in having weeds actually not evolve resistance to Roundup.  So my guess is they honestly thought it was a highly unlikely outcome.

Why did they think so, despite being smart, honest biologists? Because they weren't trained in, or primarily thinking about, evolution as it occurs in nature. They were plant geneticist and bioengineers, spending many years and countless millions of dollars to unravel the finest details of how Roundup kills plants and how to build a crop that will have resistance to it (without passing that resistance on to its offspring). That was an enormous challenge, and their success was unprecedented. They had achieved what many, even within their own company, must have thought was an impossible SciFi dream.

Surely someone was assigned to think deeply about the problem of whether weeds would evolve resistance, but surely that someone had been involved in the project for years, and was so wrapped up in the grotesque details of the genetic magic they had just achieved that no perspective was possible. In other words, they couldn't see the field for the soybeans. A person highly trained in artificial selection, and used to that way of thinking, will think of the evolution of weed resistance in those terms, despite the fact that natural selection has inherent advantages.

In hindsight, their logical errors are obvious, probably even to them. In foresight, reasonable and well intentioned people frequently fail to think of highly relevant and potentially obvious things. This is particularly likely if those things require a perspective they don't possess, doubly particularly if they are thinking deeply about the problem from a very different perspective. Monsanto had many biologists who knew about evolution, used a particular type of evolution as a tool, and thought about evolution. But my guess is they didn't have any evolutionary biologists.

Sunday, March 11, 2012

Evolution infringes upon Monsanto's patent

NPR has a useful story today by a guy who interviewed people who were involved in Monsanto's application for release, in 1993, of "Roundup Ready" crops, that is crops that are genetically engineered to be resistant to Monsanto's best selling herbicide, glyphosate, sold as Roundup. The idea, which has made Monsanto many billions of dollars, is that if the crops are immune to the herbicide, and weeds are not, fields can be sprayed liberally. Farmers don't have to do mechanical weeding, and Monsanto gets to sell them both the patented herbicide and the patented resistant seed. This set of facts, along with Monsanto acting like the faceless corporate giant that it is in defending its patents, has made it probably the most despised company among the organic farming crowd, vilified far more than competitors like ADM or DuPont.

The point of the article is that Monsanto falsely rejected the possibility that carpeting the world in Roundup would lead to the evolution of Roundup resistant weeds.

Then the story, written by Daniel Charles, continues like so:
Oops. Since then, resistance to glyphosate has emerged in 20 different weed species.
  I called up several people who were at Monsanto at that time. Why didn't people there think resistance would happen? They all told a similar story.
First, the company had been selling Roundup for years without any problems. Second, and perhaps most important, the company's scientists had just spent more than a decade, and many millions of dollars, trying to create the Roundup-resistant plants that they desperately wanted soybeans and cotton and corn. It had been incredibly difficult. When I interviewed former Monsanto scientists for my book on biotech crops, one of them called it the company's "Manhattan Project."
Considering how hard it had been to create those crops, "the thinking was, it would be really difficult for weeds to become tolerant" to Roundup, says Rick Cole, who is now responsible for Monsanto's efforts to deal with the problem of resistant weeds.
In case the holes in their logic haven't struck you, allow me to provide a quick lesson in how natural selection (or in this case semi-natural selection), as opposed to genetic engineering, works.

Engineers at Monsanto were surely aware of natural selection and its proclivity to producing resistant pests, but they considered the idea that there would be even a hint of heritable resistance in the weed populations to be highly unlikely. This is because they failed to consider the following facts:

A. They were testing thousands of highly targeted potential genetic alterations in the lab, on a few crop species, and found that almost none of them conferred significant resistance. They didn't consider that after global distribution of their crops, trillions of genetically distinct (although totally untargetted) genetic modifications (that is, natural mutations) in thousands of weed species would be tested for their resistance. When something potentially useful did pop up, Monsanto was again able to test hundreds or maybe thousands of slight modifications on that, while natural selection could within a few years test millions of potential modifications iteratively over several generations. So they didn't consider that nature's search for solutions would be far more exhaustive than theirs.

B. I'm sure engineers have a term for closely examining one type of failure risk while completely ignoring others. That's what Monsanto did. They were look hard at making plant tissue resistant.  From the same story:
Some weeds, Cole says, appear to keep glyphosate from entering the plant at all; others sequester the herbicide in a spot where it can't do much damage. Monsanto's genetically engineered crops use a different technique entirely.
So they didn't consider the possibility that some plants would simply shield their vital tissues from the toxin, the way many metal resistant plants do.

C. They assumed that because Roundup had been used broadly for several years already, and there were no known resistant weeds, weed populations simply had no resistance traits available for natural selection to favor. They failed to consider that with the introduction of their crops, and the resulting increase in usage, both the population size of the exposed weeds and the force of selection for resistance would increase dramatically.

The force of selection is a measure biologists use to ask the question, how much difference does a heritable change of a certain size in a trait (for example a 0.1% increase the probability of surviving a spraying with Roundup) make to the fitness of the individuals with that altered trait. So long as most individuals in a weed population were never exposed to Roundup, the force of selection for resistance to it was small. Resistance doesn't help much if you are never exposed. The seeds blowing into farmers fields were coming from unexposed sub-populations, and so were not resistant. When we started blanketing the world in Roundup, the force of selection increased, because most every weed subpopulation over huge areas was exposed. So their experience up to that point led them to underestimated the force of selection for resistance. And if there is one thing that evil empires should know, it is to never underestimate the force.

Friday, March 02, 2012

Google goes stupid

Yesterday, at work, I was using Google Image Search to try to find an example of a particular kind of scientific figure. I wanted a figure where any variable has been measured over ages from early in life to late in life, and where the data are U shaped (start out high, go down, then go back up) but where someone had fit a simple linear regression to these data, completely missing the pattern. I see such figures fairly often, but couldn’t remember exactly where. I also wanted examples where they had got it right and fit something other than a straight line.

So I used search terms like: “linear regression” “scatter plot” age and figure. And I got back images of babies, mothers breastfeeding, pornographic images of women (not medical or educational or artistic, despite having Safe Search set at strict) mixed with a smattering of scatter plots, almost all from papers about women’s reproductive health, breast- and cervical-cancer and baby nutrition. None of it was useful to me, and a lot had no apparent link to any of my search terms. What was going on?

At the same time at home, my wife was reading a Blogger hosted blog on women’s reproductive health and baby-care. She was using my laptop and was still signed into gmail as me. Blogger is owned by Google. Yesterday was the first day of Google’s new policy of sharing information about users of any of its services with any of its other services to help to personalize search results and the ads it shows. I was looking for figures. My wife was reading about women, their reproductive health, and their babies. I got images of babies, women’s figures and reproductive parts, and scientific figures plotting data on same. If I was interested in scatter plots related to breast-cancer, I would include “breast-cancer” in my search terms. Yesterday, I logged out of my Google account in order to get decent results from Google. This is not helpful for Google or for me.

There has been a big kerfuffle about the lack-of-privacy implications of this new policy. People say that Google is becoming Facebook, a sinister ploy to know more about you than you do. I am sympathetic to those complaints, but not particularly worried about them for my own sake. My main complaint isn’t that the new policy is evil (i.e., Facebookish), but that it is stupid (i.e., Microsoftian), in that it makes Google’s core product, Search, less useful. Google is forgetting what Microsoft has never figured out: Too many functions doing things for you detracts tremendously from the functionality of the software. If I want to sit down at a new computer and use Word, I don’t want to first have to individually turn off all twelve parts of Autocorrect and 75 other things that will change my document for me in undesirable ways. And if I want to search for something, I don’t want terms I haven’t inserted invisibly added to my search. To have the algorithm decide to include terms from a blog that I (or anyone logged into the same account) read in my search takes control away from me, and then I have to fight against the algorithm to find what I want (or, heaven forefend, use Bing). It’s like having a car that tries to drives you to a restaurant of its choice every time anyone in the car, or on the radio, mentions food. You drive because you have to, but after the tenth visit to that terrible restaurant, you wish you could just walk.

The Google–becoming-Facebook complaints are surely in part a reference to Google’s relatively new social network site, Google+. But here again, it feels to me more like Google-becoming-Microsoft. My complaint stems from their push to drive every possible bit of traffic to Google+, even if this makes their other products harder to use. Microsoft similarly tried (before being ordered otherwise by the courts) to so thoroughly integrate Internet Explorer into Windows that you basically couldn’t use one without the other. Google seems to be trying to do the same with all their products and Google+. The‘Photos’ link used to take me to my photos on Picasa. This was helpful. Now it takes me to the recent photos that people in my circles have uploaded to Google+. This is not generally useful, and makes it harder to get to my pictures. On pretty much all their products the Share button (which used to take me directly to the option to email or link to an item) now opens a window asking me to post whatever it is on Google+, making it harder to share whatever it is with the vast majority of people I communicate with through other means. I understand that Google wants me to communicate with all of them only through Google+, but as that is never going to happen, designing a product that assumes it has already happened is stupid. There are quite a few of these small things that don’t make a big difference in and of themselves, but take Google’s products, which have traditionally been beautifully designed and implemented one step closer to things I use because I have to. And once you are into “use because I have to” territory, you are Microsoftian.

Sunday, February 26, 2012

Camels (and alpacas and equids)

There are camels, at least seven of them, in one of the vacant lots adjacent to the Institute. These (the lots, not the camels) are generally dominated by garbage-bespangled weeds and scrubby little trees. Today there is a circus truck, a tent with camel stalls, and a bunch of camels happily chomping the weeds down to the ground. I've seen goats, sheep and even cows used to clear brush, but the camels seem to be eating through the weeds faster than any of these could. The garbage has been removed (hopefully before the camels were let in), and there is a man who looks more like a circus worker than a government worker cutting and hauling away the woody stuff  the camels pass by (actually just throwing it into another one of the vacant lots). It seems like by tomorrow evening they will have to move them to another lot, or bring in fodder. I wonder if the circus is paying for, or being paid for, the use of the lot. Seems like a good deal for both parties.

It is 6C (43F) and sunny, which means that Rostockers think it is summer, and are walking around, admiring the camels. Some college kids have carried their couch onto the waterfront and are setting up a barbeque.  The ice on the harbor has all melted, and the gulls and mallards are looking for handouts.

Given all this, you might rightly ask why I am in the lab on a Sunday, instead of showing my daughter the camels, or walking with my wife, considering that I have excellent student assistants who are doing all of the actual lab work. The answer is that student assistants are not allowed to be in the lab by themselves, regardless of how mature or well trained they might be, or how routine or undangerous the work. So if the animals need to be checked every day, someone has to be here every day to baby-sit whichever student is in that day. This situation has actually gotten somewhat better. For 18 months that someone always had to be me, and I worked 7 days a week unless I was too sick and had to ask a colleague to cover for me. Now I am working with two wonderful post-docs, and only need to be in the lab every third weekend. Soon another graduate student will join us, and it will be every fourth weekend. Of course, the more experiments there are going on, the longer we have to be in the lab each day, and we are at about 6 hours now, and this will increase. So while those 7 day work weeks I was working included two pretty short days, the occasional work weekend will soon mean working almost full time.
This is honestly not so bad, but I’d rather be out watching the camels eat up that vacant lot.

Update: 10 camels, 6 alpacas, 4 miniature ponies, 3 donkeys and 9 horses. Only the camels are out grazing, fodder is being brought in and more tents are being set up in the areas already cleared.

Friday, February 24, 2012

National Academy of the Extremely Vigorous

People of higher educational attainment live longer. This is widely known. Somewhat less widely known is just how far up the attainment ladder this pattern goes. People with Master's Degrees tend to live longer than those who stop with a Bachelor's. Even more longevous, on the average, are those with doctorate. But people who get a doctorate and then go get some random job don't tend to live as long as those who become tenured professors. And sitting atop this hierarchy of attainment and longevity are the members of the elite scientific academies, such as the National Academies and the Royal Society. Many people's tendency when thinking about this correlation, between attainment and lifespan, is to assume that being better educated helps one live longer. To some extent this is certainly true, and at the level of primary education, and even college education, there is experimental evidence (both true experiments and accidental experiments through policy changes) to prove this. But in thinking about the differences between groups of people with graduate degrees, I rather suspect that the causal relationship is rather different.

I'm thinking about this at present because I have had a very productive evening. Since coming home from a full day at work I've made dinner, done the dishes, played with my daughter, rocked her to sleep, folded the laundry, done more laundry and folded that also, cleaned the cat's box, organized things around the house, rinsed the drop-cloth we put under the highchair while my daughter learns to eat, cleaned the broccoli and potato bits out of the bathtub, written work emails, taken down the garbage and the recycling, climbed the 18 flights of stairs to come back up and written half a blog post. This is extraordinary for me, especially this time of year. I am almost always either coming down with something or trying to recover from it, or coddling an inflamed joint, or just feeling low energy. I lose a disgusting amount of potential productivity to being sickly. The elite academies members I know, and those who are not yet in those academies but seem likely to be in them some day, are all people who are this energetic all the time. If they do get sick, they seem to almost always be back at in after a day or two. It is rare for me to recover from a cold in less than a week, and not rare for me to be out for two or three weeks at a stretch. This is not to say that many of these people are not also smarter than me in important respects, but the trait that most unifies the really successful academics I know is their extraordinary energy and vigor. My boss, nearing his 70th birthday, and a National Academy member, hardly seems to know what it is to feel tired. He'll attend meetings on four continents in the course of a week, say how exhausted he is, and still spring from his chair to scribble equations on his whiteboard. So my belief is that people of the highest academic attainment live longest not because they are of high attainment, but because they are remarkable in their health and energy, which also allows them to produce the torrent of great science necessary to be elected to one of these societies. Alright, enough writing, I'm exhausted.

Thursday, February 23, 2012

Scandal! Scientists find error in their own results!

Last September, a group of scientists in Italy got some strange results that made headlines around the world. Their results suggested that neutrinos were traveling faster than the speed of light.

I ask you to consider the following excerpt from a BBC article that came out just after their announcement:
"We tried to find all possible explanations for this," the report's author Antonio Ereditato of the Opera collaboration told BBC News on Thursday evening.
"We wanted to find a mistake - trivial mistakes, more complicated mistakes, or nasty effects - and we didn't.
"When you don't find anything, then you say 'well, now I'm forced to go out and ask the community to scrutinise this'."
Friday's meeting was designed to begin this process, with hopes that other scientists will find inconsistencies in the measurements and, hopefully, repeat the experiment elsewhere.
"Despite the large [statistical] significance of this measurement that you have seen and the stability of the analysis, since it has a potentially great impact on physics, this motivates the continuation of our studies in order to find still-unknown systematic effects," Dr Ereditato told the meeting.
"We look forward to independent measurement from other experiments."
I now ask you to consider the opening of NPR's article reporting the news that the error has probably been found:
Remember last year, when we reported that Italian scientists claimed to have broken the speed of light?

And this, from a blog post headed "That's Embarrassing" that one of my Facebook friends linked to:
Remember CERN's claim that they found neutrinos traveling faster than the speed of light? Weeeeeell now they want to renege, blaming a faulty fiber-optic cable and timing gear for the erroneous results. Jesus -- and we're supposed to trust these people to NOT tear open a black hole and swallow earth?
And this, linked to by another friend

Ridiculous: A Loose Cable Caused Those ‘Faster-Than-Light’ Particles

We know that Einstein always has the last laugh, but this is hilarious: the faster-than-light particles that could have wrecked his relativity theory are no more. It was a mistake in the test results caused by a loose cable.
Didn't anyone from the Genius Bar tell them about the first rule of tech support? Check your cables first! Oh, scientists!

I try not to get to whiny in complaining about the state of American science journalism, as I know it is not going to improve any time soon, but this really quite lamentable. The scientists involved were faced with data that could potentially destroy the theoretical underpinnings of their field. The wrong things to do would have been to ignore the data because they are theoretically heretical, or to make a big deal about their irrefutable and earthshaking discovery. Instead they did exactly what they should have done: They announce the situation to their peers and asked for help in evaluating the situation. They did this with full knowledge that their results would probably be shown to be in error, and that when that happened they would be mocked and insulted. This is an example of science working as it should, despite a dysfunctional press. No one, no matter how well established or well funded (or named Einstein), is the High Priest of science, and everyone's conclusions have to be reexamined and reconsidered. This responsibility to skepticism extends especially to one's own conclusions.

Their results have now been shown, by them, to have probably been an error, and the message the average American is getting is that these goofy Italian so-called-scientists were just too comical to even consider the possibility that Einstein was smarter than they are. NPR's science reporting is actually usually better than most, which is why I read their articles. In this case, they went with the invented scandal.

Tuesday, February 21, 2012

The boundries of personhood

A group of academics (psychologists, ethicist, biologists etc.) have recently endorsed a statement arguing that dolphins and whales do deserve the rights of humans, based on their intelligence, self-awareness, individuality, sociality and so forth.

 A curmudgeonly old man, who was an environmentalist but hated that he was because he didn't like to be associated with hippies, once opined to me as follows on this topic, only in much more colorful language: We can't start treating whales as though they have the same rights as humans, because if we give those rights to whales, we have to give them to apes too, and if we give them to apes pretty soon we'll be extending them to monkeys, and pretty soon antibiotics will be outlawed because they violate the inalienable rights of infectious bacteria.

I have mixed feelings about slippery slope arguments generally. Letting even minor instances of objectionable predilections (sexism, racism, etc.) slide really does seem to be a problem, on the principle that once people are used to these sentiments going unchallenged, they will feel freer to get more egregious. But we can and frequently do make different rules about the treatment of different categories of animals, and there is little likelihood of the rules that now apply to the study of chimpanzees being extended to include studies of bacteria, let alone infections. My research with live animals legally requires no review by any ethics board because I am working with invertebrates. Back when I studied birds, I needed committee approval just to go out in the woods and watch birds for scientific purposes, and my friends who study humans have sometimes had to get such approval just to reuse preexisting published and publicly available data on long-dead populations.

The fact of the matter is that we can and do make arbitrary decisions, often influenced by scientific knowledge but also influenced by emotional predilections, about who and what deserve what rights and protections. Before the US Civil War, southerners quibbled with the evidence that slaves were fully human, but more fundamentally they didn't admit that this implied that they deserved the same rights as other people. These days, American conservatives tend to want to extend the full rights of personhood to fetuses, embryos and potentially fertilized eggs. American liberals often want to extend these same rights to smart charismatic non-humans. Each side sees the other as both ridiculous and morally bankrupt. The difference underlying these wants are philosophical, moral, ethical and political, sometimes economic, but not generally founded in disagreements on scientific fact. Those factual disagreements usually follow, as each side looks for ways to justify its conclusions. I don't expect cetaceans will ever be granted the same rights as humans, but as we learn more about their mental and emotional lives, I do think it will become harder to treat them little different from large endangered fish. In other words, I think we will go part way down the slope.