Archive for: August, 2011

Pipetting Diva has some bumper sticker advice

Aug 31 2011 Published by under [Et Al]

You should go check it out here. Don't say I never give you anything.

2 responses so far

On being a great dad

For a variety of life reasons, I had to take the Weer One into work today to attend a meeting that included two departments and the Dean. Wasn't a big deal, she slept most of the meeting (wish we could have switched) and when she made some slight noise, I pulled her out of the car seat and held her. People were aware she was there, but it wasn't a disturbance. Life happens and you have to pull an audible sometimes.

But as I was leaving the meeting, I got several comments. A couple people asked me about the baby and then something unexpected happened. One of my senior colleagues with whom I do not interact much, said to me "You're such a great dad." This was quickly agreed to by another colleague. Now maybe I am, maybe I'm not, these people wouldn't have any idea. I could have been on my way to dropping her off to the traveling circus*. But apparently being willing to watch your kid while fulfilling work obligations is enough to win me the distinction.

You can't read the inscription, but it says "Way to at least give half a shit, Dad!"

But it got me wondering, how many women who have to bring kids in to a meeting are considered "great"? While I will admit that my department is pretty family friendly, I have never seen a female colleague admired for just making the best of a childcare "situation".


* Obviously this isn't the case. The circus doesn't take kids until they can eat gruel.

16 responses so far

Graphic Fridays: How days get murdered

Aug 26 2011 Published by under [Education&Careers], [Et Al]

The other day I fell into the most basic n00b trap of them all: The 15 Minuter.

The trap is set when a senior colleague asks you to take on a "15 minute" task for them. It's a brilliant ploy, because you look like an asshole if you can't spare 15 minutes to help someone out, right? So you agree under the assurance that "it'll probably not even take that long". Stupid n00b.

(A) So you begin to plan for your "15 minute" task by talking to the person organizing the larger program you have just gotten involved in. (B) The organizer reveals that the group they need you to talk to is larger than expected and proposes dividing it into to two, instantly doubling your time commitment. (C) After reluctantly agreeing to two groups, you receive the itinerary and notice you are scheduled for an hour. (D) In calling to protest the doubled time, you finally get the whole story. Looks like they want you to demonstrate something specific for this dog and pony show, which of course, means you need to head into the field to get the material necessary if you want to generate any interest in the topic at all.

You didn't have any plans that day anyway, right?


3 responses so far

The Solar Sea Slug story gets.... odd(er)

Aug 25 2011 Published by under [Biology&Environment]

I've followed the scientific developments surrounding the fascinating kleptoplasty of sea slugs for a while, mainly because it's an intriguing riddle. How does an animal steal plastids (chloroplasts) from an alga and keep them alive for 9+ months, all in the absence of the algal nucleus?

If you are unfamiliar with the story, go check out this first post of the topic from a few months ago. As a quick primer, however, certain sea slugs suck out the contents of algae, then digest everything but the plastids. They then sequester these plastids in their articulated gut and can survive solely on the energy provided by the organelles for months. This might not be that surprising, except for the fact that the genomes of plastids only encode about 1/10 of the proteins required for their function. The remaining proteins are encoded in the nucleus of the algae and directed to the plastids via a protein targeting pathway. So if the sea slugs keep only the plastids, where do 9/10 of the necessary proteins come from?

In 2008, this system looked like a possible case of large scale DNA transfer from the algal nucleus to that of the sea slug when an algal gene was identified from the nucleus of the sea slug, Elyssia chlorotica (Rumpho et al. 2008). However, subsequent work by Wagele et al (2011) found no evidence of transfer in related sea slugs that show similar behavior. At the time the response was "Well, maybe gene transfer is specific to E. chlorotica", so transcriptome studies were launched on this beast.

But now the results are trickling in and the story has taken an odd twist. Deep sequencing of the E. chlorotica genome not only fails to reveal any strong evidence of active algal genes in photosynthesizing sea slugs, but none of the algal genes previously identified as putative transfers are detected (Pelletreau et al. 2011, Rumpho et al. 2011). So what is going on?

Although the 2011 Pelletreau and Rumpho papers claim that horizontal gene transfer (HGT) can not yet be ruled out, the probability of algal genes playing a central role in this kleptoplasty is beginning to look highly unlikely. Sure, it is possible that those genes follow different expression patterns than we would expect, but the facts are that the plastids still need to function and the proteins need to come from somewhere. There is no protein fairy that replaces critical cofactors and enzymes in the middle of the night. If we can't detect the mRNA, it is highly unlikely that the nucleus is harboring the genes of interest.

That leaves us having to consider alternatives to traditional cell biology, which is fascinating in it's own right. Are the sea slugs using enzymes to store the proteins in the gut, releasing them to the plastids as needed? Are there protein-stabilizing properties of the sea slug gut? If so, how does the slug recognize the plastid-targeted proteins while digesting the rest? Another curious aspect of the story is that the plastids consumed by the sea slug are typically encased in four membranes, but the outer two are digested away by the slug, possibly simplifying the protein delivery system. This also has implications for the original HGT hypothesis because if the sea slug nucleus acquires genes that have targeting peptides for four membranes, they may not be processed correctly when only two membranes remain.

When this system was first descibed there were many questions. The HGT story in 2008 made it appear as though there might be an incredible adaptation that give rise to kleptoplasty, but in the last year the story has once again become muddled as new data have failed to support the HGT hypothesis. IMO, genomics alone is not going to solve this one. Someone is going to have to get freaky with some protein isolation work and figure out what is going on in the gut, and where. As a non-model system with no genome sequence, it is not clear when this will happen, but my guess is that the answer will be worth the work.


Rumpho ME, Worful JM, Lee J, Kannan K, Tyler MS, Bhattacharya D, Moustafa A, & Manhart JR (2008). Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica. Proceedings of the National Academy of Sciences of the United States of America, 105 (46), 17867-71 PMID: 19004808

Wägele H, Deusch O, Händeler K, Martin R, Schmitt V, Christa G, Pinzger B, Gould SB, Dagan T, Klussmann-Kolb A, & Martin W (2011). Transcriptomic evidence that longevity of acquired plastids in the photosynthetic slugs Elysia timida and Plakobranchus ocellatus does not entail lateral transfer of algal nuclear genes. Molecular biology and evolution, 28 (1), 699-706 PMID: 20829345

Pelletreau KN, Bhattacharya D, Price DC, Worful JM, Moustafa A, & Rumpho ME (2011). Sea slug kleptoplasty and plastid maintenance in a metazoan. Plant physiology, 155 (4), 1561-5 PMID: 21346171

Rumpho ME, Pelletreau KN, Moustafa A, & Bhattacharya D (2011). The making of a photosynthetic animal. The Journal of experimental biology, 214 (Pt 2), 303-11 PMID: 21177950

5 responses so far

Is there a dark side to the breast feeding movement?

Aug 23 2011 Published by under [Et Al], [Science in Society], Uncategorized

This will be my last baby-related post for a while, but I wanted to talk about breast feeding. Yes, I know, a dude talking about breast feeding is about as popular as a hunk of raw meat at a vegan tea party, but I'm actually more interested in the culture of breast feeding than the act itself.

With our first child we did the typical first-timer thing where we read all sorts of stuff ahead of time. We developed a birth plan that was focused on doing everything with drugs and we were ready... and then shit happened. There were complications, things came out of left field and we had to roll with it. In the end, things worked out well. We had a healthy mom and baby, a decent birth experience and not much to complain about given the circumstances.

But if there was one things that we were gonna do, it was breast feeding. I mean, if you don't breast feed, your child is basically going to grow up a moron with slurred speech who is sick all the time, right? I mean, these are facts*! Except maybe when you actually look at the science (see "Problematic Science" section). Nevertheless, there is no doubt that breast feeding is beneficial to both Mom and the baby, so away we went.

Except sometimes the body doesn't cooperate. Sure, it can take some time for a mother's milk to come in, but did you know that some women's milk never comes in? Or when it does, the level never comes close to reaching the child's needs? We didn't. But we found out the hard way. Five days of a screaming hungry child and little sleep. When the visiting nurse came to our house our baby was dehydrated, had lost almost 15% of her birth weight** (and she was already small) and had jaundice. We were told that if we went another day of weight loss that we would have to bring the baby back to the hospital. We decided we had to get this kid some food, no matter how we did it. Turned out that despite continued effort, my wife's milk never really came in and it would have been a huge mistake to stubbornly continue down the breastfeeding only path.

But why did it take us so long to reach this rather obvious conclusion? Because of the 1950s. Starting in the 50s there was a move away from breastfeeding in the US (A solid summary of historical trends can be found here) and in the 1970s there began a push back that has resulted in the resurgence in breastfeeding rates. But like any issue where strong opinions are involved, sometimes numbers get a little skewed, arguments become more extreme and "common knowledge" spreads unchecked. If you look around at many pro-breastfeeding websites and take them as The Truth, you would come away thinking that not breastfeeding your child ought to earn you jail time and if you give your child anything but a breast, it will forever spurn you and your nipples. And so new parents will put themselves and their babies through a lot to avoid being Those People.

And as one of Those People, let me tell you that the reaction from many people when you reveal that you are not breastfeeding is full of subtle assumption that you are a bad parent. There are two types of typical reactions:

1) You are selfish and don't care enough about your child to put the work*** into making breastfeeding happen.

2) You don't know what you are doing and let The Man force you into making a bad decision for your child****.

Combine these reactions from many people you talk to with the emotions of a new mother who already feels like she has failed and it is easy to get to a bad place very quickly. Nothing like having judgment heaped all over you as a new parent for something you can't control.

But the thing is, our first child is not a toothless sloth. I know, I'm as shocked as you are. And with the second we have managed to use formula to supplement through an extended period of slower milk production to get things going a little bit this time around, and neither the bottle nor formula turn out to be baby crack. In fact, we seamlessly go back and forth!

When we started talking round after our first child, we were surprised at how many women mentioned that they had milk supply issues with at least one of their children. For some, it works out after some struggle, for others it doesn't. But in the end, the point should be having a happy child and parents, not adhering to some doctrine. While breast milk has been clearly shown to provide benefits for your child that a formula diet cannot, it is not always an option for all mothers. However, the alternative is not sentencing our child to a lifetime of playing catch up, despite the ads.

*As an aside, people love to throw around random stats during the entire process of child rearing, most of which are total bullshit and completely self-serving to the internal narrative of the Stats Provider.

**In the US, 10% is the threshold where they bring the baby back in.

***And it is work in the beginning.

****It only took four comments on a post where I mentioned milk supply issues, in passing, to get one of these.

27 responses so far

School spirit!

Aug 22 2011 Published by under [Et Al]

It's starting. Despite a bit of time until the school year begins, there is a tangible change on campus. The collective anticipation of the student burden that approaches has a distinct feel and those organizing the earliest activities can be seen buzzing about.

One distinct harbinger of the fall studential return is a massive influx on university-emblazoned clothing items to the book store - to the point that they have a special overflow area to contain the additional stock. Indeed, these items get consumed as fast as they are unboxed and this is one of the few universities I have worked at where university-themed clothing is worn by an astonishing percentage of the people crowding it's walkways and classrooms.

Perhaps because my academic career has never taken me to places where sports is a major campus focus, I have never been one to wear my affiliation on my sleeve, so to speak. I have owned clothing associated with my undergraduate institution, but in three institutions since, I don't recall buying any university clothing. However, I have noticed at my current institution that faculty regularly wear Employment University garments, or adorn their cars with stickers to the same effect.

Am I missing some benefit of getting wrapped up in school spirit, or are other university employees out there similarly non-plussed by being draped in someone's artistic representation of some obscure mascot choice?

13 responses so far

Why we can't all move to Canada

It's almost cliche at this point. Every time there is an issue in the US you can almost count down the seconds until someone decides to claim they are moving to Canada. And what's not to like? Socially liberal*, universal health care, curling and funding rates so high that they give you a grant for crossing the boarder, right?

The current situation with NSF funding doesn't appear to be any different in this regard. Low funding rates and the recent application changes have people once again invoking the tired "Why can't we do it like Canada?" Look, I love our neighbors to the North as much as the next person, but there are things you can pull off when you have a population the size of California that just won't work in the US. If you need a primer on the Canadian system, a good one is here, but the summary is as follows: The NSF equivalent, NSERC, maintains 60% success rates (currently); grants are for 5 years; the annual total is usually small by US standards, roughly $20-50K; students are not typically supported off grants; there is no overhead take by the university**.

On the plus side, 5 years provides stability and the high success rate means that labs do not typically burn out due to lack of funding. The flip side of that is the career trajectory of new PIs can be skewed. First time grants are often between $15-25K over a five year stretch. This is your proving time to show you are worth a bump at your first renewal, otherwise you my find yourself locked into <$20K budget for A DECADE. But back to the first 5 years, at $20K/year you're not hiring a postdoc or tech. More likely you'll have two students at a time, who are on a relatively short leash when it comes to reagents. Maybe this is an issue for your science, maybe it's not, but don't forget that all your conference travel, publication costs and in some cases, student summer salary, come out of that $20K. You can only hold a single NSERC grant at a time, so unless you can go to foundations or CIHR (the NIH equivalent), you're locked into that budget for the duration.

If you make proverbial lemonade, you might get a bump in year 6, but there is no guarantee of this and I've had colleagues with similar records get doubled or maintain the same budget for their second grants. Additionally, if you do get money outside NSERC, you're almost guaranteed to get short shrift from NSERC in future applications in favor of those reliant on NSERC, regardless of your record.

The result, however, is that people doing science that costs a bit more end up having to pick away for the first 5 years, rather than come out with guns blazing. Start-up packages are also considerably smaller than the US, and buying equipment for the lab is often tied to applying for CFI equipment grants. These also have a high funding rate, but there is the risk that you'll have a largely empty lab for 6-12 months. All of these factors make it more difficult (though people certainly do it) to really take off as a junior PI.

But let's assume that we can deal with a drawn out career arch if the result is more people funded. Here's the bigger problem: the universities.

I already wrote this in a comment on the post linked above, but entire funding structure of universities would have to be reworked. The issue with the Canadian system is that it CAN’T work in the US without massive changes to how universities operate. US universities use the overhead from individual grants as a major portion of their budget, whereas this is not the case in Canada. If NSF started funding at $30-50K/year, not only would labs who have to support students (+ tuition) off that get little to no work done, but universities would lose a huge amount in revenue (not to mention that the Uni would take 1/3 of that money anyway).

On the surface you can just say that the universities will have to compensate in some way, but it also means that most larger universities will focus their hiring on NIH-fundable PIs, even more than they already do. Basic science in the US would then suffer BOTH from being underfunded and phased out of university hiring priorities. The end result would likely be a situation where smaller universities do basic science and larger ones do NIH stuff, which is not ideal. Let us also not lose sight of the fact that "basic" research is a critical springboard to medical research, often in unexpected ways.

Changes at the funding source would have to be matched with changes at the university level, which are unlikely if NIH is unaffected. I am not at all claiming this is impossible, but merely that we have to take into account the larger structure before we tout another system as being "more fair" or "better".

Much in the same way that people want universal health care but don't want higher taxes, it's important to realize that the implications of different systems have far reaching effects that may not be obvious on the surface. If all you see if "60% success rate!!!!!" you are missing the larger context.

There's no free lunch out there, folks. Decide what the priorities are and then figure out how we pay for them.

* On average. Alberta hasn't received the memo yet.

** Although this is changing slightly and Canadian universities are getting creative about ways to "charge" for certain facilities, resulting in some grant money claw-back.

11 responses so far

Graphic Fridays: Exponential Growth?

Aug 19 2011 Published by under [Et Al]

9 responses so far

More musing on the NSF Bio changes

Aug 18 2011 Published by under [Education&Careers]

So we've all had a day to think about what these new changes in the NSF Bio application process will mean for us. Other than the stuff I brought up yesterday, one of the big things that sticks out to me that we're going to have to adapt to is the preproposal. I don't mean as a step in the process, but rather where the bar is for getting past this stage. Will preliminary data need to be demonstrated to the extent it is currently required? Will that be the major hurdle, or can we pay some lip service to this and sell the idea more? How do we compress a proposal idea into 1/3 the space and make it convincing?

To a certain extent, NIHers went through this transition a few years ago when the application for major awards was shifted from 25 to 12 pages, but this is a bit different. We'll be justifying 3 years of work in less than 4 pages of text (page one is just for personnel and don't forget that Broader Impacts has to show up in the preproposal too). The new RFA indicates that the following 5 criteria must be met by the 4 page preproposal:

"Conceptual Framework" or "Objectives" or "Specific Aims"
"Rationale and Significance" or "Background"
"Hypotheses" or "Research Question (s)"
"Research Approach" or "Experimental Plan"
"Broader Impacts"

Economy of space is going to be huge. Do you include figures? How hard do you sell the approach vs. the significance? Obviously this is going to be case-by-case, but there will be enormous amount work involved in creating preproposals for each planned January submission rather than updating an existing proposal.

Another unresolved question is whether the panels that screen the preproposals will have the same membership as the panels that read the full proposals, or not. To my knowledge, neither IOS or DEB has a history of carry-over in panel membership, so does that change or not? Will there be feedback associated with accepted and rejected preproposals or will there simply be notification of the decision? Particularly in cases where the preproposal is accepted, the feedback from the pre-panel might be counter to the opinions of the full panel if they are different. There is some potential here for some messy situations.

What are others seeing that concerns them most?

2 responses so far

NSF BIO decides to screw new investigators

Aug 17 2011 Published by under [Education&Careers]

So I was happily going through my email this morning and opened up one of those "daily digest" emails from NSF. Ten seconds later my keyboard and screen were covered in coffee spray.

NSF BIO has been looking to make some changes to their review process for a while. The MCB division of BIO recently announced that they were going to an 8 month cycle, whereby there would still be two deadlines a year, but proposals could only be submitted to one or the other. They also limited the number of proposals that a person could be listed as PI or co-PI to one per cycle. Odyssey has a summary of the changes here.

Now, the IOS and DEB divisions of Bio have decided to see those changes and raise them. Both divisions released new core program solicitations today (DEB and IOS links) changing the annual format of proposal deadlines. In both cases, 5 page preproposals will be due in January on the dates that were formally proposal deadlines (the 9th and 12th, respectively). Those preproposals will be reviewed and full proposals will be by invite only in.... AUGUST!

That's right, a mere 7 fucking months between pre- and full proposal submission. Invited proposals will only be accepted in August, annually. So NSF basically stole all of the things that people hate about the USDA proposal process and decided those would be great to implement.

In addition, individuals may only be listed as PI or co-PI on two proposals annually. Now, a key factor here is that these are within-division rules, so if you can apply to multiple divisions you may be able to skirt this rule. This also does not apply to special programs like AToL or CAREER. But if you are limited to a single division, it's time to start dumping collaborators.

The group this is most going to affect, IMO, is new investigators. With the national and institutional focus on multidisciplinary research over the last 5 years, most younger scientists have been encouraged to pursue areas of research that are highly collaborative. Now NSF is pulling the rug out. As a PI trying to get your research program off the ground, are you going to work on collaborative proposals or concentrate on the bread and butter of your lab's focus if you are limited to two proposals annually? Hmmm, let me see...

It also means that there will be an enormous lag between proposing the work and getting meaningful feedback. I'm sure the preproposals will be reviewed in a timely fashion, but in order to get feedback on the full proposal it will be at least a year from inception to reviews.

Also note that the current July deadlines already mean that we don't get reviews back on proposals until Nov-Dec. Pushing this deadline to August will almost certainly mean that reviews on full proposals will not be available in time for the preproposal stage in January if the full proposal doesn't get funded. Therefore, if you submit a preproposal in January 2012 and it gets invited for a full proposal in August 2012 but doesn't get funded, you likely will not be able to resubmit that same (revised) proposal until January 2014 with the hope of seeing money by January 2015!

Labs go extinct in that amount of time.

Yes, BIO will be achieving the goal of reducing reviewer burden, but the cost of this move could be substantial if the bar for tenure remains the same for NSF funded individuals. Laughably, in retrospect, NSF has fought hard against those who have called for capping the overhead amount. The argument has been that they did not want to devalue NSF research in the eyes of universities by making NSF grants less "profitable" on a dollar to dollar basis than NIH grants. This new policy, however, has the possible side effect of making NSF research a riskier proposal for new investigators - at least from a time to first grant perspective. Don't be surprised if the further marginalization of NSF funded research at major universities takes a big leap forward over the next 5 years.

31 responses so far

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