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.

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.

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.

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.

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.

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.

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.

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.

Culturing culture

I am supervising/mentoring/collaborating with two post-doctoral researchers (a.k.a. postdocs), and greatly enjoying the process. They are both smart, hardworking and enthusiastic, and, unlike me, talented experimentalists. I am good at proposing experimental designs, and at inventing or improving upon experimental apparatus, but I managed to get through all my years of training as a biologist without ever being taught the nitty-gritty of laboratory work. I like to make things up as I go along, and work on twelve projects at a time, paying sporadic attention to each, and you can't really do experiments that way. But these two post-docs actually know what they are doing in the lab. It is impressive to see how thoroughly they train the students, how carefully they document their doings, and how well they know their organisms. As a grad student I started working with rotifers with almost no prior knowledge of rotifers, and without any advisor who knew rotifers. I read the literature, but there is a deep cultural knowledge about how to care for aquatic lab animals, with lore and practice around each group, and I had none of that. These two know, and it is wonderful to watch and learn.

I, flotsam.

Certain relatives of mine cling to the fantasy that I will be able to decide where I get a job, so as to live within a few miles of them. While the sentiment is appreciated, and shared, the reality is that I have almost no say in where I end up.

Let's review a few facts. First, the US economy is still in the shitter, if slightly less deep in than a few years ago. Lots of people, regardless of their industry, are moving wherever for whatever job they can get. Maybe there is some profession where you can just up and move where you want and be confident of making a living there, but I'm not sure what profession that would be at this point.

Second, even in good times, academics can almost never pick a city and get a job there. For hundreds of years academics have been moving to whatever University has a position for them. I'm reading a book about Alexander von Humboldt, who was one of the greatest scientists of the late 1700s and early 1800s, and even he keeps going from country to country looking for a patron and encountering academics working far from their own countries. There are extraordinarily few academics who can simply contact a University of interest and based on their scientific reputation be confident of getting a job there. Once you've won a Nobel Prize your chances are good. Barring that, good luck.

Third, I have done what most of the academic establishment says scientists should do, but very few fully do, because it makes publishing and job-hunting that much harder. My work is so damn interdisciplinary and specific that I am unlikely to fit the particular job description a small disciplinary department at a college or university is likely to write. I am on an email list for an online bulletin board for evolutionary biologists called EvolDir, and every few days I get an email for some position somewhere in the world that they are trying to fill. Here are a few of the most recent entry-level faculty positions:
•"There are several openings for Bioinformaticians and Software Developers at the University of Glasgow (UK)."
•The City University of New York seeks candidates with expertise "in tropical ecology, biogeography, evolutionary ecology, and conservation biology."
•" Tel Aviv University (ISRAEL) invites ... applicants who apply modern approaches to investigate fundamental problems in the general area of Plant Ecology. "
•UC Riverside "invites applications for a faculty position in plant evolutionary developmental biology."

These are positions I would bother applying for. This is not to say that I won't find anything, but rather that even if Near My Relatives U does decide to advertise for a new professor, they are more likely to be looking for an expert in the genomic analysis of primate fecal samples than they are a developmental evolutionary demographer. When I am ready to apply for positions, the question will not be, "Is that biking distance from my relatives?" but rather, "am I plausibly qualified for that position and is it a place where my wife is willing to live?" If it is, I'll need to apply. It is most likely that positions I do apply for will be among the relatively few broadly defined positions in evolutionary biology, with no further disciplinary restrictions. I very much approve of such broad-net casting, but it tends to lead to many hundreds of applications, as everyone in the field qualifies, so my chances with any one such position are slim.

If the economy were to improve dramatically, I could plausibly limit my search to within 1000 miles of my family. As it is, that limit will be about 12000 miles.

How I got stapled to a live turkey, and other fond memories of California

Round about this time of year I usually start making a list in my head of all the reasons I should probably not live in northern Germany much longer than necessary. One of my complaints is my general lack of opportunity to observe and interact with wildlife. I spent the better part of a decade doing biological field work, spending most of my time in the general proximity of wild animals. Sometimes it was more proximate than "general proximity" would suggest.

One day early in grad school, I was on my way into research museum where I worked, when I was stopped by the museum's eccentric old preparator, who was on his way out and wanted my help on I knew not what. I ended up on the beach with him and an armed National Park ranger using a carving knife to remove the head and fins of a dead whale that had washed up, for reasons that were not entirely explained to me at the time. I think the skull may have wound up in our museum's collection, but the ranger kept saying something about things not ending up on the black market.

Another time, my friend Alan wanted help catching and marking the wild turkeys he was studying. He would set up big walk-in traps baited with grain on cold mornings, and trap a whole flock of turkeys at a time. Then he would pull them out one at a time, measure them and attach a patagial tag to their wings. My job was to hold the birds' wings still while he attached the tag. Well it was quite cold and wet and my fingers were numb, so I didn't immediately notice that the rivet had gone not only through the bird's wing (as it was supposed to) but also into my hand. It took perhaps a minute to detach me from the turkey without further injuring either and bandage my hand before we could move on to the next turkey.

More often, my wildlife fix came in the form of bird-watching or lifting rocks to find lizards or salamanders. It was a rare week in California that I didn't get to do some wildlife viewing, and nature was as close as my back door. Here I live near the middle of a city with a long cold dark winter, and the life of a lab and desk biologist just isn't as adventurous. There is a city park across the street which in summer hosts some interesting if overfed animals, but especially this time of year I feel the absence of wildlife. Of course there is no guarantee that the next place I live will be so wild as is Berkeley (or preferably more so), but I can hope.

Spanning the vastness

When I was but a lad, my siblings and I used to accuse my father of knowing everything, a charge he would always deny, observing that even excluding those things which are not known to anyone or are secret, and restricting ourselves to academic knowledge, there is more to know than any one person or any thousand people could possibly know.

To see why this is so, consider the sheer volume of scientific literature being produced. ISI Web of Knowledge, an online tool used primarily by scientists for finding scientific literature relevant to their work, indexes the contents of over 23,000 academic and scientific journals. Many lesser known, newer or otherwise less main-stream or traditional journals are not indexed at all. One needs to go to other databases to find information published in books, or in dissertations, or, or, or.

Like my father (as I am in most things), I find myself far too mortal to know any meaningful fraction of anything, even if we restrict ourselves just to academic biology. I'd say there are roughly 8000 peer-reviewed journals in which biological work is regularly published, and if you add up all the papers I skim through, it is probably the equivalent number of pages of the output of two or three of these. The papers I read in detail if assembled together would surely make up much less than the output of a single journal. And I put more time into reading and therefore less into writing than is optimal for my career.

One result of this is that I frequently find out that there exist thriving sub-disciplines of biology of which I have almost no knowledge. For example, only last week I for the first time heard the word "metabolomics." Google Scholar lists over 6000 papers in the last year on this rapidly expanding field about which I know no more than I could guess based on the name.

My knowledge of transcriptomics was quite as absent three years ago. Transcriptomics is the study of RNAs in the cell, generally in the context of gene expression patterns. I became interested in transcriptomics because I proposed that mortality risk during embryonic development would be highest at those stages at which gene expression patterns were changing fastest. I was a doctoral student at the time, and my adviser asked me if there was any way of testing this idea. I had to admit I didn't know if it was possible to test because I didn't know enough about the field I have since learned is called transcriptomics. The answer is that yes, there is a way of testing the idea, but it will cost a couple of hundred thousand dollars, and require collaboration with people who read different journals than I do. I will never be an expert in transcriptomics, but I can find a colleague who is, but has little knowledge of evolutionary demography, and invite him to collaborate on a project that combines our expertise. And this is why science can be a somewhat unified pursuit despite having far more product than one person can read even the titles of.  

I referred in my last post to one of my advisers at Berkeley, and one of my all around favorite human beings, Ron Lee. Ron would always advise me to think about my relative advantage, by which he meant I shouldn't just work on the most interesting or best questions, as there are far too many. Rather, I should choose among them by considering which questions I was better placed, given my strengths and resource, to answer than was anyone else likely to work on the question. Ron's advice has always served me well, and so I do consider this before starting any project. Frequently, as with this developmental transcriptomics and demography project, my relative advantage arises from the fact that I am combining two fields separated enough that no one else is likely to ask the question any time soon. Evolutionary demography and developmental biology do not, as a rule, talk to each other. Many fields of biology have almost no communication with each other, leaving vast unexplored interdisciplinary territories (unless that is all in some set of journals I haven't come across yet).

Emissions of the aged

Projections of future carbon-dioxide emissions are complicated. How will energy consumption habits change as societies get richer or more urban? What mix of sources will we be getting our energy from?

My friend and colleague Emilo Zagheni decided we should make the calculus that much more complicated (and informative) by also asking how the aging of the population will influence carbon outputs. A demographer's demographer, which Emilio surely is, is never happy with any calculation that does not include age-structure in one way or another.

This article in the Economist summarizes what he did and what he found. As people get older, they tend to consume more and more, emitting more and more carbon, until 65ish, at which point consumption tends to start declining. See the graph, and the analysis, in the Economist, or the original in the journal Demography (2011) pp 371-399.  The punchline for the carbon-watcher is that the changing age-structure will tend to increase carbon emissions until about 2050, after which point such a large portion of the population will be above 65 (I'll be 73) that the age effect will begin to marginally decrease emissions.

I should finish with a quote from Ron Lee, Professor of both Demography and Economics at UC Berkeley, who both Emilio and I studied under. Ron was one of the inventors of the widely used Lee-Carter method* (1992) for forecasting future mortality patterns. Seventeen years later, I asked Ron how well his forecasts for the first 17 years matched what had actually happened in those years. He cocked his head slightly to the left, sighed sagely and said, "Well, demographers are well aware that our projections don't always fair so well in a complex world. But we console ourselves with the knowledge that we do much better than the economists."


* The original article has been cited more than 1000 times in the peer-reviewed literature, and modifications are used by the US Census Bureau, the UN, and so forth.

Suddenly crustaceans

I don't have a taxonomic specialization, and I'm happy with that. I've worked with or dug deeply in to the literature on hardwood forest trees, midges, several groups of birds, frogs, rotifers, primates and Hydra (the polyp, not the mythical beast). I've probably read more of the literature on beetles in the family Melyridae than any other non-entomologist who knows almost nothing about beetles.

I've now gotten to the point in my career where I am organizing a research group and serving on people's committees, and suddenly and unintentionally, I'm all into crustaceans. I'm supervising a post-doc and a doctoral student and on the committee of another student all working on different Daphnia projects. Daphnia are the model organism for crustaceans. I've got another post-doc working on barnacles (which despite their outward appearance as adults, are very much crustaceans, and go through not one but two amazing metamorphoses before ending up attached to ships, rocks or whales). This particular barnacle, Balanus improvisus was first described by Darwin (1854) in his giant book on barnacles that he wrote to procrastinate publishing On the Origin of Species (1859).

I've still got projects on Neurospora a fungus best known for ruining your bread, on Hydra, and on primates (including humans) going, but most of my time at the moment is crustacean focused. I suppose I will have to learn the basics of carcinology. Yes, that does come from the same root as carcinogen and carcinoma.

11-hour

One of our laws in the U.S. requires that federal paperwork that people have to fill out be a bit longer than necessary in order to inform us that the federal government is mandated by law to reduce unnecessary paperwork, and to provide an estimate of how long it should take to deal with the particular piece of paperwork.

I'm preparing a grant application to the National Institutes of Health, and have spent the last month trying to figure out the rules, regulations and customs. They provide a helpful 264 page guide to filling out the application form, with links to more information online. This guide estimates it should take me 11 hours to prepare my application, not including the part where I design my research. It also advises me that I should read the whole guide, and the various additional information (including a very necessary glossary) before beginning to fill out the forms. A friend of mine, who recently looked at this instruction book and thereupon decided not to apply for NIH funds, suggested that anyone who could read and comprehend all 264+ pages in under 11 hours with enough time left to fill out the forms should probably just be acknowledged as a genius and given whatever money they need for their work.

I certainly don't blame NIH for having a lot of rules, or putting them in a book. They have a huge number of people asking them for money, the responsibility to make sure all the applications are dealt with fairly, and the need to comply with a very large number of laws on many topics. All sorts of special cases and exceptions arise, and they need to have guidance on everything (although I have already come across several places where one just has to know how it is done, generally by asking people who have done it before). So you can't really blame their helpful but understaffed staff. However the 11-hour estimate should probably be reexamined.

Anyway, I'm learning, and the next time I write an NIH application, it may take me only 11 hours to understand the rules, provided they haven't changed them too much. The sad part is that the proportion of applications funded continues to decline, even as the length of the application instructions increases. I'll distract myself from thinking about that by reading the 33 FAQs about the Modular Grant Application Concept.

Can anyone think of model organism genera starting with I,J or Q?

Arabadopsis

Bufo

Caenorhabditis

Drosophila

Escherichia

Felis

Gallus

Hydra

I

J

Klebsiella

Loligo

Mus

Neurospora

Oikopleura

Phodopus

Q

Rattus

Saccharomyces

Trichoplax

Ustilago

Vibrio

Wolbachia

Xenopus

Yersinia

Zea

A, alligators all around

They say that the distance in inches between an alligator's eyes and its nostrils is equal to the length of the whole animal in feet. This behemoth hangs out by the fishing dock in Loxahatchee National Wildlife Refuge feeding on discarded bait fish and who knows what else. My best guess is 14 inches nose to eyes, which would make it not unheard-of big but certainly exciting-to-canoe-past big.

It is amazing to think such an invulnerable top predator (at least within the refuge) started out nearby as a scared little snack for herons like this:

Authorship code

I'm writing a paper with two of my students. Well, I'm writing it with one of them and another one did a lot of work on the statistics. But today we had to straighten out the order that the authors would be listed in on the paper. This can be a contentious issue, and I know of cases in which papers did not getting written at all because the authors couldn't agree on who got to be listed first. Some big multi-author papers simply list everyone in alphabetical order to avoid the fuss, but then Dr. Aardvark always gets to be first author. Some journals have a little section where each author's contribution is described, but they usually end up saying something uninformative and false like "all authors contributed equally."

I came up with most of the ideas in the current paper, put things together, decided who would do what, etc. My student did much of the lab work and is doing much of the actual writing. Given this, most biologists would propose what I did, and what my student objected to: She (as the person doing the writing) should come first, I (as the senior person on the paper) should come last, and everyone else (in this case meaning the statistics student) gets sandwiched in between. This was very counterintuitive for my student; she thought I was trying to minimize my own role by putting myself last. In fact, it is a step up for me to be writing papers in which I am in that last position. I remember this being counterintuitive for me the first time it was explained to me. I was a college student, and a boss said that he'd make me second author on a paper. I said something to the effect that I'd be glad to be even last author, which I thought was being humble, but he took it as me saying the paper had been my idea. We straightened out the miscommunication but I didn't end up being listed as author on the paper. That the last author spot (at least in biology) signifies the senior author is a code biologists internalize, and I had to think back a long way to figure out why my student objected to me being last author. I explained, she reluctantly believed, and now it is settled.

Oh give me a home, where the apple-snails roam

Retirement communities are, by design, fairly sterile places. Much of south Florida is covered in huge gated spreads of nearly identical buildings with neatly trimmed lawns leading down to pleasingly curving shallow canals so that every apartment can have water views. It is uniform, controlled, boring. But all those networks of shallow canals catching lawn fertilizer and Florida sun provide habitat and highways for rapidly growing aquatic plants, which feed aquatic invertebrates and fish. With relatively few retirement community residents catching their own fish, this leaves the fish to grow as big as want.

Or at least it used to. When I was a kid visiting my grandparents in Century Village, I rarely saw any wildlife around the wide place in the canal (referred to as a lagoon because it increases resale values) behind their apartment.

When I was a teenager and my grandmother was widowed, the lawn by the water was occupied by a flock of Muscovi Ducks (plant eaters), Cattle Egrets (which eat mostly insects picked from lawns) and the very occasional Great Blue Heron, which eat only small to medium fish. My aunt inherited the same apartment, and my wife and I brought our baby daughter to visit her this winter. Our first morning there, jetlag woke us early. Standing by the lagoon was a flock of Wood Storks. Walking past them in the water's edge was a flock of White Ibis, trailed by a Tricolor Heron.

On the far bank an Anhinga spread its black wings to the sun. A few feet away lay a huge dead fish, heavily built and probably 80cm long, partly eaten by something. What could kill a fish that big, drag it up on the bank and eat only part of it? Walking the banks we found the shells of numerous Apple Snails, so named because they are as large as the fruit. Apple snails don't come up on land by themselves, so something must have carried them up, presumably to eat them. In back of the next building over, beyond the Great Egret and Little Blue Heron, I could just see something moving on the bank. I thought it might be a dog (not allowed in Century Village) but then I could see it was two long low animals chasing and wrestling with each other. They jumped in the water and swam as no dog could. River otters! A pair of very large river otters chased each other, making circles in the reflected condos. The remains of several large fish, each only partly eaten, attested to the successful hunting they had been having in the canal.

Four Turkey Vultures sat around one such plate of sushi as others circled and swooped, their wing tips almost brushing the screening of enclosed patios. We cajoled my aunt, her bad ankle throbbing, to come out onto the lawn with us for a closer look at the otters. We crept closer to them and the fish they were snacking on until they raised their heads and hissed at me, at which point we backed off.

All this wildlife, carrion, birds and their poo on cars, giant snails, etc. are pretty clearly not what the designers of Century Village, and south Florida's thousands of other retirement communities had in mind. Nevertheless, I think most of the residents are probably happy to have so much nature on their lawns. I doubt all those telescopes and binoculars sitting in the screened patios were for spying on the other retirees.

Is this all good for the wildlife populations? Clearly they would have been better off if the wetlands had not been made into retirement communities, but given that they were, I'd guess that learning to exploit those communities is to their advantage. The water in these canals surely has all sorts of runoff from lawns and parking lots, but if the birds feeding in it can still breed consistently, they are likely to have a feeding habitat that no one will drain, pave or burn. If things get too rough in the nearby Everglades, they will have a retirement home ready.

The end is neigh!

When I start working on a project, it is always interesting and exciting, otherwise I wouldn't start working on it. Developing ideas is fun, narrowing down the question to just the core issue is challenging, building an apparatus or simulation or whatever feels productive and creative. But I also have to actually write a paper which frame the whole thing in a useful way, which means reviewing and summarizing the relevant literature, which is boring unless I actually have something novel to say about that literature, other than what my new experiment or analysis or whatever shows. And I have to make my paper, which is always interdisciplinary in some way, fit into a particular journal, most of which are tightly disciplinary. So I'm much better at starting papers than finishing them, and I have a tremendous backlog of papers to get out. It is therefore a great relief to have just sent out what was originally (three years ago) a response to another paper in which I saw some methodological shortcomings, that turned into a broad comparative analysis of human and primate demography, and ended up as a review article submitted yesterday to an anthropology journal. One of my co-authors is a bone fide anthropologist, so I feel confident that we at least refer to most of the right papers. I'm also confident that our points are valid and important and the paper generally well written. But mostly I just feel happy that if all goes well I will soon no longer have to work on this paper.