Archive for: November, 2010

Are society memberships kinda like herd immunity?

As the year is drawing to a close, I've realized something. Due to some strange financial road blocks at the start of the year, I put off renewing my regular memberships to the three societies I normal pay dues to. Then I got busy and forgot to send in the paperwork, despite having it prominently on my desk. All three memberships include a print journal that I also did not receive all year.

So, you would expect I really missed out on some stuff this year, no?

The reality is that I didn't miss out, which is also part of the reason my motivation to renew was fairly low. It's not that I don't support these societies or don't want to be involved, it was more that there was no downside to forgetting to renew. I still have access to all the journals online and get email table of contents for them all. I even still remain active in a service role for two of the societies as a member of the editorial board of one and chair of a committee in another. The fact that I didn't drop a couple of hundred bucks to be an "official" member seems to have had zero consequence.

Part of the reason for this was an unusual summer schedule that took me to some conferences for other societies, rather than making my normal rounds. The meetings I typically go to overlapped with these others, making impossible to get to all of them. For that reason, my membership in my normal societies slipped under the radar in a way that likely would not have happened in other years.

Nevertheless, it does make me wonder a bit about the utility of society memberships to the individual. I should note that I am not advocating that people not renew their memberships because I realize that if everyone opted out of membership a society would go under - hence the title of the post. I also plan to renew my membership in the new year, but if one was interested in answering the question "what would happen if I didn't renew my membership for a year", it would seem that the answer is "nothing".

12 responses so far

The bloated proposal

I have to gut one of my bread and butter proposals. I don't want to do it, but it has to happen. I've talked to my PO and to a few other people, and shifting the approach I'm going to take with this proposal is the only thing that makes a lot of sense and will give it a better shot at getting over the funding hump.

It took me a little while to figure this out because I kept thinking that they just wanted a little more "preliminary" data, and if I could provide it, all would be good. But with this project, the preliminary data I kept piling on was like thinking that I could just give a junkie a little more smack and they would be fine. In the time this proposal has been submitted, I have already completed two of the original objectives and published one of them (all while changing the focus of the proposal to reflect these advances). Despite this, the panel wanted more, which made me realize that the particular route I was taking was only going to be satisfactory when either A) It was done and I could make it pretty clear that I wasn't full of shit, or B) changes in technology made the process more trivial to do. Both of these things are happening, but not soon enough. So when one side of the fortress is impenetrable, its time to try the back door.

The change means that I need to pull out a substantial amount of text that is no longer relevant to the new aims. It is never fun trashing text you worked hard to create, but one thing I did not expect was realizing I should have done some of this sooner.

I have gotten enough feedback on this particular piece of writing over a long enough time that pieces of it are starting to look like a mash up of the original and various responses to criticism along the way. It has gotten cumbersome and crowded. There is text in there that no longer needs to occupy the space it does, but has remained as an ancient relic, left there because it was once a cornerstone to a building that no longer exists. In the last round I was so focused on getting our new data into the proposal that I didn't prune out things that were de-emphasized. As painful as it is to delete whole sections that took time to assemble, I am amazed at how much better the whole thing is going to look.

Part of the text removal is in response to being a panelist, as well. My current proposal is pretty dense, with just a couple of figures - the exact type of proposal that would cause me to sigh when I picked it up at 11:00pm with the hope I could get it reviewed before 1:00 so I could get some sleep. Something tells me I am not the only reviewer in this situation, so why do I want to make someone else sigh when they flip through my proposal? The slash and burn routine will open up space for more figures and allow me to let the text breathe a bit and maybe even put some space between paragraphs. I don't need to cram 17 pages of stuff into 15 pages because reviewers probably spend less time reading packed proposals, not more.

This is going to be a lot of work, but I like this proposal and I think I would like it as a reviewer, even at 11:00pm.

One response so far

PLS and the tale of the three grants

There once was a wee lad by the name of PLS. One day he was skipping through the forest of science when he came upon a house in the middle of the woods. He knocked but no one was home. Being naive to the frightening number of guns owned in the US, he let himself in and made himself at home.

As he looked around this seemingly familiar home, he realized that there were three of everything, but of varying sizes. Displayed prominently over the fireplace was a large picture of three grant proposals. "Oh." he thought. "These proposals must live here." The pictured showed one proposal that was big and mostly complete, with just a few parts needing editing. The second proposal had a lot of its parts, but needed some significant writing to fill in the holes. The littlest proposal was juuuuust getting started and merely the remnants of a previously gutted proposal.

PLS walked over to the table and saw three objectives sections. The first one was big and robust. It had obviously been thought out and worded carefully. The second one had all the parts, but needed some work, and the poor third one was a mere skeleton of a real objectives section. The littlest one was juuuuust getting started and required some serious attention.

On the counter by the sink were three preliminary data sections. In contrast to the objectives sections, all three of these looked pretty strong, but all three had many new pieces that were lumped together in a range of cohesiveness, from incoherent to reasonably accessible. Provided a decoder ring, one could juuuuust make out how they made the proposal better.

PLS walked up stairs and found three beds, each with methods and expected outcomes sections strewn across them. The first was too big and rambled on for pages and pages. The second one was the right length, but needed some serious editing, but the third one was juuuuuust a mess.

At this point PLS was tired. He curled up into the big bed (because for a wee lad he was freakishly large) and drifted off to sleep for a few minutes before being woken up by the yells of a 2.5 year old, saying "Daddy! I have to pee! Now! Pee pee coming out!"

The End

7 responses so far

The sexiest thing in cooking...

Nov 20 2010 Published by under [Et Al]

Is deglazing a pan with red wine. Discuss.

6 responses so far

But those grant reviews are unreasonable!

One of the hardest things in the granting game is dealing with the reviews. There's always some conflicting signal and some jerk who didn't read the section on the exact thing they claim is wrong with the proposal. While the natural reaction is to blow off the reviews that appear to be blind to half your proposal, after I sit with the reviews for a bit I am always amazed at what they tell me about what I wrote.

There's the obvious things like lack of clarity. If a couple reviewers all bring up the same point that you thought you addressed, there's a good chance you either didn't make the case you thought you were making or that you need to clarify what you wrote to better guide the reviewer to the intended conclusion. This kind of stuff plagued me early on and it took a while to craft the right way to push an idea that might be controversial.

Another point which has taken me longer to appreciate is the "unreasonable amount of demanded data" issue. Ever gotten a review back where a reviewer or two start asking for the world on a plate? I've had reviewers demand things that would require 3x the typical NSF budget and the invention of new technology. On first read I thought, "What an asshole, that's not even possible!", and while it is still not possible to meet those demands, after a while I began to realize that the demands were so high because that was the level of data the reviewers thought I would need to answer the questions I was proposing. Now who's being unreasonable?

I'm not at all saying that every reviewer has completely valid points all of the time, and often there is a middle ground between what you think needs to be done and what the reviewers are going on about. But I think the proportion of reviews that have something important to be heard is very high. The issue is tuning your hearing to the right frequency.

6 responses so far

Negotiating your start-up package in non-medical biological sciences

Yeah, I'm a bit early on this since we are currently in application / interview season, but it's something I have been thinking about a decent amount recently. Why? Because there are things I should have asked for that I didn't and a few things that I did ask for, which have saved my ass. Having done a postdoc outside the country, I wish I had had a bit more information than I went in with, as some of my assumptions turned out to be false.

So, based on my experience and the collective experience of the readers here, I thought we might be able to put together a decent guide for those of you who will hopefully be in the position to negotiate in a few months. The tricky thing is trying to put a number on this, because there is enormous variance between institutions. Instead of talking numbers, I would like to talk about categories of things to ask for. These should be widely applicable, with variable values depending on your field and institution.

Listed based on priority:

EQUIPMENT
This is obviously one of the big ones. You need to have the cash to set up your lab in a way that allows you to get the things done you need to. Everything from major equipment to chemicals to the stupid little spatulas you use to weigh those chemicals out with needs to be thought of. I did it by wandering around my postdoc lab and writing down everything I saw. It is amazing how many little things you can forget / take for granted. List them all.

How you approach putting a number on this category depends on how nit picky the person you are negotiating with is. In my case, I made categories of stuff (e.g. "freezers and refrigerators"), thought about how many I needed and looked up some ballpark prices. In most cases, you are pretty safe going with the list price, because every vendor will crawl out of the woodwork to give you a discount when setting up a new lab. If you use the list price as your guide, you'll have between 20% and 50% of that money left over when you actually by the item. That is a good thing.

In some cases you will be offered the use of shared equipment for big things or possibly that the university will buy you a specific item or has one they will give you. In this case, GET IT IN WRITING. And I mean the exact model number you want and everything. If they say they will buy it, get a timeframe in your offer letter. Even if you are negotiating with the nicest people in the world, get that shit in writing! Decide what you can share and what need to be dedicated to your lab and make sure you get the latter category. There is nothing more stifling than having to wait for shared equipment when you are just getting things to work.

CONSUMABLES
This is another category that you can budget list prices for and come out ahead when vendors battle for your shiny new start-up money, but put the funds in this category to keep you going for longer that you think. I would say at least 3 years is a good idea, 4 if you can get it. Again, gloves to weigh boats, figure out what you need.

PEOPLE
There's no use having a stocked lab with no one in it. Figure out support for your people. Does your department offer TA support for students? If so, get a few lines of support committed to your lab. Do you need a technician? Get salary. Same with a postdoc. You may not be able to ask for the moon and the stars, but decide what you want and fight for it. In this funding climate, best to ask for one more year than you think you will need, as well.

And don't forget yourself. If you are in a 9 month appointment, ask them to cover summer salary for a few years. If you get grants to cover it instead, I'm sure they won't mind.

SERVICES (added)
This was one I forgot and have added in response to comments. In most cases, it would be a good idea to add in the costs involved with data production, if you require outside services or expensive methods.

SPACE / RENOVATIONS
This is a category that some people take for granted and I've seen some get burned. It is common for a school to show you a space when you interview. Is that the same space you will inhabit? Maybe, maybe not. Will there be renos done? Probably. But when will that happen? In some cases I hear people complaining about never done customization a year or two into the job. At that point, you've either found a work around or are too set up to allow a work crew in the place to mess it all up. Again, get a time frame in writing!

TEACHING
If you can help it at all, don't teach in year one. There's a lot going on and a million things to figure out already, having to do all that with teaching responsibilities on top of that makes life a lot tougher. Ideally, getting out of teaching in year 1 and then getting some softball grad class in your specialty in your third semester before taking on a undergrad class in semester 4, is not a bad way to ease in.

TRAVEL
Do you need to go places to collecting things for your research? Do you want to go to conferences in your first couple of years to get the word out that you've moved and you're a big kid now? Budget it. What about your lab peeps? They'll probably want to go to conferences too, or maybe they need to travel for workshops or collecting. Don't forget to make a category for this!

COMPTERS AND SOFTWARE
This is a funny one, because sometimes money needs to be in a specific category to buy computers. Find out about that. It may be just for grant funds, but worth asking. In any case, you'll need things like computers for you and your peeps. Printers and ink. Back up systems? Servers? What about software you use? A lot of it can be pricey, just look how much the Adobe suite is. And that's before you get to specialized proprietary software.

I'm sure there are some things I am leaving out that others can bring up. It's a daunting process trying to figure out everything you will need to get going, but it can also be a lot of fun.

15 responses so far

I know you think I'm awesome, just ask me.

Nov 15 2010 Published by under [Education&Careers], [Et Al]

When did it become okay to ask people to write an opinion about them for you? This practice is socially acceptable, how? Seriously, is there anything worse than asking someone to write you a reference letter and then having them foist the responsibility right back at you? The message is, "Yes, I'll support you, just as long as it doesn't require an ounce of my own effort". I can see situations where this is alright to do, but in most cases it just kinda sucks. Sure, I'm putting together a whole proposal, but I would love to write your opinion of me as well. Thank you for your support.

Dude, fuck. Sigh.

18 responses so far

Perspective

Nov 14 2010 Published by under [Et Al], [Life Trajectories]

I've bitched a bit recently about how much I am not enjoying this academic year, but I think a bit of perspective is not a bad idea. We have neighbors who are good people and have kids who are in a financially tight spot. The neighbor's kids (who are roughly our age) have been squeezed by the economy and find themselves with two daughters and one part time job between them. Both were employed before the economy shit the bed, but it's a different world now. They no longer have their own apartment and are struggling to make ends meet.

Our daughter spends a good amount of time with their kids, so we know them well enough to know how things are going for them. After months of trying to make a go of things the way they have unfolded, they have made a drastic choice. Dad is going to Afghanistan.

There are many reasons to enlist for military service, many of them honorable and well thought out. However, it pains me to watch a young couple with two young kids decide that their last option is placing a member of the family in harm's way, in the hope that he will survive and that the benefits of military service will help them stem the tide of problems they have faced.

As pointed out recently by CPP, the trend of military service being more populated by the less economically privileged is nothing new. Fundamentally, I knew this, but seeing it played out in front of me in such a blatant fashion brings a lot home. I can't say that I agree with why we're in the wars we are in, but I can't see a reason not to support those who are there, fighting on the order of our country.

3 responses so far

Some parasites decide working with their host is more their style

Nov 12 2010 Published by under [Biology&Environment]

ResearchBlogging.orgThis post was chosen as an Editor's Selection for ResearchBlogging.org

Apicomplexans. The term probably means little to you unless you have ever faced the prospect of contracting Malaria. Even still, it is unlikely that you are aware that Plasmodium falciparum, the causative agent of Malaria, is a member of a large group of parasites, classified as the apicomplexans. Other members include Toxoplasma gondii (Toxoplasmosis), Cryptosporidium parvum (Cryptosporidiosis) Trypanosoma brucei (African sleeping sickness) and Trypanosoma cruzi (Chagas Disease), among others.

Apicomplexans, in general, are nasty bugs that infect numerous animal species as parasites and pathogens. At ~6000 described species and many more yet to be discovered, the apicomplexan lineage is possibly the most diverse lineage of parasites known. They also have an unlikely origin, betrayed by a miniaturized organelle, called the "apicoplast". This organelle was known for many years before it was shown to be a highly reduced plastid in the mid-90s, and later determined to be derived from an endosymbiosis with a red algae. While no longer photosynthetic, the apicoplast carries out cellular functions, such as heme, fatty acid and amino acid biosynthesis for the cell. It maintains a genome, but the vast majority of active proteins in the apicoplast are encoded in the nucleus and targeted via a 5' leader signal on the mRNA and a complex targeting pathway. The apicoplast is essential for the cell and has, not surprisingly, drawn a lot of interest as a drug target.

Until a couple of months ago, the apicomplexans were thought to be entirely obligate parasites. However, Saffo et al. (2010) discovered a likely exception in an unlikely place. Members of the genus Nephromyces have long been known to inhabit the renal sac of certain small sea squirts (Molgula, Fig. 1). While living in this rather undesirable location, they feed on the kidney stones of the sea squirt and release nutrient back that the sea squirts utilize. For a long time these invaders were thought to be fungi, but they have some very unfungal characteristics, such as a biflagellate stage of their life history (fungi are, like their relatives the animals, uniflagellated) and a worm-like form that can be found in the sea squirt blood stream. DNA work done by Saffo and colleagues shows very clearly that Nephromyces are actually members of the Apicomplexa.


Fig. 1. Molgula sea squrit, home of Nephromyces. Image source.

Interestingly, this is not a case where these symbionts or mutualists (it is not clear yet*) are early diverging members of the apicomplexans that may have gotten out before the whole group went parasitic. Instead, they are nested squarely in the midst of their nasty cousins, indicating a revesion from parasitic to a friendlier life style - an event that is exceedingly rare in nature. So how and why did they do it.

Well, to start with, Nephromyces have apparently lost the apicoplast. There are other apicomplexans that have accomplished this, so there is no direct link between loss of the apicoplast and loss of a parasitic life style, but it is interesting. Second, Nephromyces has either lost or significantly reduced an apicomplexan structure called the rhoptry, which is the secretory structure used by infective stages of apicomplexans to gain entry into host cells. Third, and perhaps more importantly, the Nephromyces themselves harbor a symbiont. Their symbiont is a bacterium, which is thought to aid the Nephromyces in digesting the kidney stones it uses for nutrients. Nephromyces has therefore traded in its relic plastid and parasitic life style for its own bacterial symbiont and symbiotic relationship with Molgula.

This last point is particularly interesting, because the transition from parasite to symbiont is, as I pointed out above, rare. The basis for this is thought to stem from the specialization (from genome to morphology) required to be an effective parasite. Once you go parasite, you never go back. So this third party involvement is intriguing because the bacterial symbiont of Nephromyces may have allowed it to exploit a new niche and shirk the evolutionary path that it seemed predetermined to follow.

At its very core, the interaction of two organisms that results in one being inside the other can only go one of two ways - either the internal cell takes over as a parasite or the internal cell is enslaved as a symbiont. The interplay between Nephromyces and the bacterium it harbors should provide clues into two key evolutionary pathways by virtue of what the bacterium supplies to Nephromyces, which has allowed it to go from the parasite that controls its host's cell, to the symbiont that is controlled by its host.

* Nephromyces are not vertically passed from parent to offspring, but need to be taken up from the environment each generation. Therefore, they fall closer on the symbiont spectrum to the dinoflagellates found in coral than obligate intracellular symbionts like the Wolbachia found in aphids.

Note added in proof Carl Zimmer also has a post up about this paper. Go check it out for a different perspective.

Saffo MB, McCoy AM, Rieken C, & Slamovits CH (2010). Nephromyces, a beneficial apicomplexan symbiont in marine animals. Proceedings of the National Academy of Sciences of the United States of America, 107 (37), 16190-5 PMID: 20736348

4 responses so far

But it's just an hour!

Nov 10 2010 Published by under [Et Al], [Life Trajectories]

Time change. Something I have never had trouble with before. Turn the clocks back in the fall and forward in the spring. Yup, got it.

Except this year. I don't know what the hell is different this year, but the time change threw a King Kong sized monkey wrench into my house this year. It started with the Wee One and trickled down from there. She normally wakes up around 6:00 +/- 15 minutes. She's pretty good about this and I can count on one hand the number of times we have had to get out of bed earlier than this since she was about 6 months old.

Until this week.

Our first tip off should have been that she suddenly was possessed by a she-devil, because the kid wouldn't listen to a thing starting on Sunday. Tantrums, general craziness and just doing things because she knew it would push our buttons. Every child has times when they do this, but this was constant. Like, do we really want to have another some day, constant.

Come Monday, she started waking up early - in the 4's. Early in the 4's. I can handle something in the 5:00 range, but 4:00ish. Nope. No good. We battled with her on Monday and kept her up as late as we could, but Tuesday brough another O dark o'clock wake up and another long day.

The flip side of that is the my wife and I are going to bed super early because we're getting woken up at 4:30, by MOMMA! DADDA! We were literally in bed at 8:30 last night and completely unapologetic about it. That means I'm not getting work done in the evenings and we barely have time after getting the Wee One to sleep to chat and spend time together before we're unconscious.

Today brought some relief in that the Wee One actually slept in, but of course we woke up uber early in anticipation of the yells. That they didn't come is some comfort, though perhaps not today as we drag through work again.

One hour. That's all it took to destroy the fragile harmony of our house life for a few days.

8 responses so far

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