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.