Archive for: September, 2010

The interesting genomes are almost gone!

Sep 29 2010 Published by under [Biology&Environment]

So I was minding my own bloggy business the other day and ran across a link at the John Hawks weblog to the discussion we were having the other day about press announcements pre-empting publishing. While reading, I came across this gem:

I think genomics has come to an inflection point -- organisms whose genomes are obviously of some utility, but which have not yet been subject of a whole-genome sequencing project, are getting scarce. It's not enough to sequence a genome, if you want to do glamor science. You have to have some, you know, science in there -- pushing theoretical understanding in some way.

I was going to leave a comment there, but it's one of those comment-free monoblogues, so we can discuss this here instead. Whereas I agree with the second part about needing to find something interesting in a genome and do a thorough analysis to get it into a glamor journal, the first part is what made me stop and say "WUT?" This is the kind of stuff that drives me nuts, as I have mentioned before because what is really meant is that we're running out of 'interesting' animal genomes to sequence. If you ask me, we hit that point a while back, but there are a shit-ton of interesting genomes out there we have virtually no idea about.

Depending on who you believe*, there are probably 5-7 'supergroups' into which all eukaryotes can be classified. Of those groups, 2 (or 3, again, based on classification scheme) have not a single published genome sequence and many major lineages within those groups are also unrepresented. We have few or no genomes to use when investigating some of the major innovations in eukaryotic evolution. We know virtually nothing about ecologically important (and truly bizarre) organisms, like dinoflagellates, at the genomic level. To say that interesting genomes are getting scarce is to admit that your view is "if it ain't animal, it's crap", which is a pretty sad statement for a biologist.

I'm not suggesting that we all go out and find a bizarre beast to work on, but simply that we allow for the possibility that there is important science happening outside of animals (and even plants, on a bad day). There is even the chance (though not a requirement) that the discoveries in Other organisms could advance the science in animals. You never know what unusual cell might change the way we look at fundamental cellular processes.

Hey there, I'm Tetrahymena. We probably haven't met, but there have been dozens of critical discoveries made using me as a study subject, including Nobel Prize winning research catalytic RNA and telomerase. But, you know, whatever. Oh, did I mention I have two nuclei that are different forms of essentially the same information, but function completely differently? Other than all that, I'm boring as hell.

*The fact that there is active debate on the major groups of eukaryotic organisms should be half decent evidence that we need to more broadly sample organisms rather than sequencing 1000 of the same genus.

17 responses so far

Why don't you just pay them more?

Everybody thinks they are underpaid. It's true, and this sentiment probably even scales with the more money someone makes. We see it on public display in sports all the time and I'm sure it happens in the business world just as much. Most people that do a specialized job feel like they have outplayed their contract.

In the academic science game, this is certainly true. No one feels like they get paid enough, especially after years of training. Grad students don't have a lot of take home salary, and while each level above them is an upgrade in pay, academics is not a place to get rich. There's been a discussion at DrugMonkey about grad student pay and relative comparisons, but that's not what I want to talk about today.

I'm more interested in why scientific trainees are not paid more*. Many people seem to think it is just a matter of the PI of a lab either not caring or being stingy. While undoubtedly there are plenty of uncaring and stingy people running labs, there are constraints on people who are neither, as well. This particular post was partly spurred by a comment by LabSpaces overlord Brian Krueger on one of Gerty-Z's posts, in which he stated:

I think a lot of professors are stindgy bastards. It always really pissed me off when I was in a lab where the PI would brag about how much money he had to waste on new computers or whatever at the end of the fiscal year and yet the undergrads in the lab are unpaid and the techs haven't seen raises in years. I say pay your good students and pay them well. Good people are really hard to find and the "compensation" of training is such a ridiculously arcane idea. Sometimes people need to eat too. And in this case, I think you're right. A student shouldn't have to choose between debt and research, especially if the PI can afford to pay them.

Now, to be fair, in response to my comment that I will elaborate on here, Brian did clarify that he was talking about a lab in which the PI genuinely did seem like a douche. But I do think this sentiment is held by a lot of students and postdocs, as evidenced from a couple of years reading this here blogosphere.

So what are the constraints on pay?

Well, the most obvious is grant funds. I realize that the typical trainee or technician doesn't care where their money comes from, but the reality of their PI's situation is relevant to the question. If we think about a postdoc, for example, the salary is only one part of the equation. If a PDF makes $45K / year, their benefits are roughly 60% of that, or $27K. Together, that's $72K / year from a budget of a grant, but it gets better because in the submitted budget the PI has to factor in the university overhead. Now you're looking at $72K X 55% (or so), which means that the hit to the grant budget is a little more than $110K / year. I know that I am in the minority of science bloggers in that I am primarily NSF-based in my finding opportunities, but I think people might be interested to take a look at the NSF funding info page and to get a feel for the median annual size of grants by NSF organization. If you don't want to click on the link, I'll spoil the surprise and tell you its in the $110K-$120K range. For BIO, it was $143K in 2009, but drilling down a bit you will see that even that number is slightly misleading due to some bigger money programs in the mix. If you look at DM's post from yesterday on NIGMS at NIH, the median funding level would appear to be $220K per year there. You can see where this is going....

Students, despite popular belief, are no bargain on a grant either. Some departments subsidize them in a significant way, but if not, you're talking a $25K salary, plus benefits (in the summer), plus tuition (no overhead paid on tuition, at least) and O/H on roughly $30K. All in all, about $60K / year. If you are writing an NSF budget and want to include a student, postdoc and actually do some work, publish it and talk about it at meetings, things get interesting.

So why can't a postdoc get $5K more? Because $5K in salary is not $5K on a grant, it's (($5K X 1.6) X 1.55) = $12,400 X 3 year = $37,200. I don't know about everyone else, but I struggle to keep my budget within what has been suggested to me as a fundable range. Adding almost $40K is not an easy thing to do because we are in competition with similar proposals that may require less funds. If your labs runs on multi-R01 NIH fuel, a $5K raise for three postdocs for only three years means someone gets one year less to work in the lab. If you draw the short straw, would you rather have two years with an extra $5K in your pocket each year, or that extra year at $40K?

Another issue is unions. Whereas unions may be to the advantage of the whole, IME they can be smothering to a talented technician who deserves a solid raise. In many cases a substantial pay increase $5K-$10K can only be accomplished with a new job description that needs to be opened up for applicants and can be taken without question by a more senior individual from that union who possess the same title elsewhere. How many technicians or PIs are willing to risk that?

Graduate student unions also put restrictions on how much students can get paid. Although they ensure that students have a minimum salary, get raises and have a collective voice, they don't allow for much flexibility in what can be paid to a student. Make no mistake, I think removing grad student unions would result in a worse situation for grad students, on the whole, but if you are going to complain about pay, your union is the place you should start.

And we haven't even gotten to the issue of competitiveness. I would bet that most people reviewing grants would tell you that they don't take into consideration what the proposal budget is, but I bet they are not telling you the whole truth. If the budget seems reasonable, no one pays attention. But, what if one investigator budgets $5K more per year in a three year proposal for a student, tech and PDF than someone else proposing something not to far off. The first proposal is going to come in $100K (15-20% of many NSF budgets for that amount of time) more than the other, and in less the science in the first one is substantially better for one reason or another, that is going to be noticed.

Finally, having grant funds and having money for salary can be two different things. While start-up funds are not categorized, grant funds are. Money in the computer budget, for example, is gold because you need to justify money in that category with a special form that needs to get cleared at you agency. Money earmarked for foreign travel and equipment is similarly guarded. A budget can therefore roll over a substantial amount of money from one year to the next without actually having any dollars available for salary.

I am writing about this because I had no idea how research budgets really work when I was a trainee and of course I could have used more cash in my beer fund pocket, but from the other side of the desk, it isn't always that easy. Unless the overall budgets for proposals is allowed to make a jump (and at 10% funding rates, where is that extra coming from?), I'm not sure where the extra money is going to come from to give grant-supported trainees a substantial raise.

*I'm interested in my professors aren't paid more too, but that's a topic for another day

40 responses so far

Women's health writeup

Sep 27 2010 Published by under [Science in Society]

Today we have a special series of posts on women's health and the absurdity of claims in mainstream media. There will be a special stream dedicated to this today on the front page and Sci at Neurotic Physiology has a round-up post where you can read about the origin of this series and also find the different blogs that are contributing today. Go check it out.

One response so far

When did announcing science become the same as publishing science?

When I was a postdoc, I used to make a Friday morning ritual of browsing through the latest issue of Science while drinking my coffee and listening to one of my favorite music podcasts. It was one of the highlights of my week, but that ritual has been long since buried by the simple fact that I just don't have time during the day to casually read through a whole journal.

But this morning, I tried. I didn't get all that far, however, because one item in the News of the Week section caught my attention and sent me looking around at other sources as well. Maybe I have just been oblivious to the subject of the article because it is not my game, but I nevertheless found the piece on Stephan Schuster getting "scooped" in his efforts to sequence the genomes of both the cacao tree and the Tasmanian devil. Why this article was so interesting is all in the nature of the scooping.

When I think of getting scooped, it means that another lab has published the major findings of something I am working on before my group was able to get the paper out. I don't think I am alone in that definition, though I haven't checked Urban Dictionary. Instead, Schuster was "scooped" because two other labs announced that they had sequenced these genomes. Uh, okay. So fucking what? According to the article, this is a devastating blow to Schuster's group, even though they have the cacao paper submitted and they are already analyzing the Tasmanian devil sequence. My guess is that they are significantly ahead of both rivals at this stage and will get their papers out first, so why is this a big deal? Science quotes Schuster as saying:

"With what happened yesterday, I don't believe in scientific publication anymore," says Schuster, who thinks work shouldn't be publicized until after peer review. "We tried to be a good citizen, ... and we lost."

You lost? What? Okay, okay, I can see how the initial big publicity would have been cool and all, but aside from a very small circle of people, who is going to remember which group made the announcement? No one. Most people will remember hearing that an announcement was made and then see the paper in a month or two and say "Hey, that chocolate genome is out. Cool." Schuster's group will get the citations and the other groups will be forced to publish their results in a less GlamorEleventy!!! journal and run all the comparative analysis. I guess I'm missing where Schuster "loses" here, unless this has more to do with the initial round of applause than anything else. In fact, they even get to be smug about how much further ahead they are:

The Penn State-CIRAD group sequenced the Criollo variety of cacao, assembling 76% of the cacao genome into its 10 chromosomes and placing 82% of the 28,798 genes along this DNA. "We were at the point of the [Mars-USDA] press release about 6 months ago," claims Guiltinan.

What also seems ridiculous to me is that there are TWO groups sequencing either of these genomes. I can understand the race for the human genome and maybe even things like fruit fly and Arabidopsis, but since when did the Tasmanian devil fan club go all cut throat? And I like chocolate as much as the next person, but two genome sequences*? It's hard to tell whether this is competition or lack of communication, but either way it seems like a giant FAIL to commit the duplicated resources. If it's the former it's just stupid and if the latter maybe it's time to think about a mechanism by which people could list what genomes are being sequenced (and not in a something-I-want-to-do-one-day-and-this-is-a-way-to-pee-on-it, kinda way. Things actually on the machine.).

We also see the whole making data public before it is analyzed thing raise it's head again.

While Schuster was fretting about his group's Tasmanian devil work being overshadowed, his colleagues working on the cacao genome were scrambling to prevent the same thing from happening to their project. The rival Mars-USDA collaboration announced that it had assembled the sequence and opened a Web site to provide other researchers access to the data.

It's one thing to have your own data released to the public right after assembly, but this is someone else's data from the same organism being put out there like a Vegas buffet. I can see this being an issue, but if you are way down the road on the analysis end, don't these announcements just light a fire to get the paper out ASAP? Statements like the one by Schuster above, might be warranted if the other groups published the data ahead of their group, but if anything, doesn't the announcement just add some buzz to the publication?

Let's wait for the papers before we start the pouting, no?

*BTW, the fact that Mars was a partner in the chocolate genome project (the second one) is something I find hilarious. Mmmmmm genom-nom-nom. Alright, maybe it's just me.

24 responses so far

Found out

Sep 22 2010 Published by under Etc

Dear Finance Office,

I never thought you would catch me, but your diligence has paid off. To truly understand my crime, we need to go back a few years to when I was an undergrad. You see, at that time all I wanted was $46.72 worth of random supplies from Home Depot. But in my lowly life as an undergrad, this was out of my reach... so I plotted.

First, I got myself involved in research between my second and third years of college. I worked many hours of two years to produce a thesis, a couple of papers and admission to graduate school. I left my home country, family and girlfriend and went to get a PhD with a well respected member of the scientific field I wanted to pursue. It was a hard decision, but I had my eye on the prize: $46.72 in Home Depot goods.

I spent two years doing the long-distance relationship thing in different countries and time zones before I married my girlfriend, who moved to a new country with me. She knew how important my dream of Home Depot supplies was to me and I owe her a lot for being willing to move her life. After 5 years of graduate school, I had my PhD, but still no university purchasing card to abuse to my own selfish ends.... so I plotted.

I started a postdoc at a new university and started a family. I wrote grants. I wrote papers. I did research and supervised others doing research. I went to meetings and gave talks. When the time was right, I sent out job applications. LOTS of job applications. I got some interviews and some went better than others. I chose Employment University in no small part because they offered university purchasing cards.

I toiled at building up my lab for two years and even sat through your three hour 'training' session that was like a long winded parental speech about responsibility and how closely we would be watched. I endured much, but I was so close.

I used the Pcard for all sorts of things, diligently keeping receipts and lulling you into feeling like I was up to the task. I was never late, never lost a thing. Always crossing my t's and dotting those i's.... and I plotted.

Finally, I thought I had covered myself well enough to get away with a crime over a decade in the making! I went to Home Depot and carefully chose my precious items, ensuring they added to my envisioned total. I purchased them with my university card and when it went through a nearly wept in joy. I rushed out of the store, clutching my hard sought items to my chest, laughing manically. I thought I had won.

But no.

Your sharp eyes caught my missing receipt and the accusations started. You sent me emails in blue enlarged text! I knew I was doomed, and no amount of explanation was going to make up for the fact that there is no receipt. Letters were written, promises were made, and my Pcard was nearly revoked. I would estimate that ~$400 in employee time was used to rectify my egregious flaunting of the Pcard rules and regulations and I am now under double secret probation.

But for a few brief moments, as I held that $46.72 in Home Depot supplies in my hands after so much work, it all seemed worth it.

And I would have gotten away with it if it weren't for those meddling kids.

15 responses so far

Repost: How day care will be the death of me

Sep 20 2010 Published by under Etc, LifeTrajectories

It is merely September and I'm already on my first bought of anti-biotics. All the kids who were out of day care for the summer are back and the Wee One already has pneumonia. Of course, you would never know it, save for an occasional cough, but I'm wiped out. Seemed like a good idea to bust this post back out from just last spring.

Day care is a necessary evil if you have a two income family. Unless you have relatives close by who are willing to entertain your child while the two parents are at work, chances are you have to rely on day care. It can be expensive and a huge hassle, but there are not a lot of options.

There are good things about day care, such as your child getting to play with their peers for much of the day. This can lead to learning a lot of things they would otherwise not be confronted with at home. Children at day care also have to get used to being with non-parents for much of the day, which one could argue helps them when their parents need to leave them with someone to get something done or to go out for a night. A lot of day cares also go to great lengths to take what is understood about how children learn and incorporate that into daily activities. All of these are good things.

But daycare has another effect on your life. Before we sent the Wee One to daycare she almost never got sick.

The Wee One, before day care.

We had the normal run of one or two colds a winter as a household, but nothing major. But day care changed all that. Day care is apparently where every cold and flu goes to party. It's like the runny nose equivalent of Burning Man and we have our very own vector from that source. It's like living with the monkey from "Outbreak".

The Wee One in day care. This is actually the look we get every afternoon when we arrive to take her home.

This winter the family has been a revolving door for colds. Every time one sweeps through and leaves us for dead, there is another one at the door. I'm pretty sure I have been healthy for a grand total of 8 days since November and my wife has been hit harder by each cold than I have. Day care is probably taking a year off of our lives, and we're not even getting to play with play dough! The thing I am most excited about this spring is the chance that the time between colds will lengthen as the days do.

7 responses so far

The fastest way to a man's heart

Sep 18 2010 Published by under Etc

"Daddy, I love you."

2 responses so far

Are spousal hires a tool for faculty retention?

Sep 17 2010 Published by under [Education&Careers], LifeTrajectories

The subject of spousal hires is always a contentious issue. There are those who rankle at the thought (unfounded assumption in many cases) that an individual might get a coveted tt position simply because their spouse was desirable for an advertised position. IME, the spouse is often as or more qualified for a faculty position, but the sheer ratio of available positions to qualified people out there has meant either that their spouse found a job first or that their spouse landed an offer in a more desirable location. There are, of course, a hundred permutations of how this can work, but my point is that I have rarely seen an instance where the "trailing spouse" is inept or lacks the experience to get hired, but is anyway*.

Like it or not, the nature and rarity of tt jobs means that spousal hires are going to be an issue and there are numerous blogosphere electrons dedicated to the discussion of whether spousal hires are "fair". I am less interested in that question** and more interested in whether, from a university standpoint, spousal hires can and should be used to increase faculty retention?

I think this is particularly plausible for mid-tier universities, and here's why. Given the choice between two offers, a single position at a top-tier university and a position for both spouses at a mid-tier university with some potential, I would guess that a decent number of couples would chose the latter. From the university's perspective, they're getting at least one and possibly two highly competitive faculty members who are going to increase the university research profile. After a while, this is going to pay dividends.

Let's face it, long distance relationships or long commutes for one or both partners sucks. You're never going to get the most out of a faculty member if their home life is being made more difficult because their spouse is either un- or under-employed, or works in a distant place. By refusing a spousal hire, a university is basically getting less than full effort from someone they just hired AND upping the potential of that person leaving for a better situation that includes their spouse. I am not advocating for departments having spousal hires foisted upon them for the sake of the university***, but if done correctly and as a concerted effort, it might be a very effective strategy.

*I'm sure some readers will weigh in with anecdotes refuting this.
** For the record, my opinion is that barring a beach of ethical practices, candidates don't get to decide what is "fair" in the hiring process.
*** The university would obviously have to be willing to commit resources to this strategy and the ever-present issue of "space" would not be an easy one to solve. But for the creative administration, perhaps this could work.

20 responses so far

Co-post: A conversation on the dangers of field science

I'll be honest, I've been thinking about this post for a while, but didn't really know how to approach it. Every time I tried to put thoughts down it seemed to me that it came off sounding like "Look how fucking tough I am! I face danger for science!" when in fact I am neither particularly tough, nor is what I do particularly dangerous. But CoR and I started talking about field science the other day and parts of that discussion seemed like a natural post. What makes it more compelling this time is getting the perspective of another person who does different work and deals with different dangers, so hopefully between the two of us we've put something coherent together. In any case, the slightly redacted conversation below. We would be interested to hear from others who spend time in the field.


When I was but a wee graduate student I did a *ton* of field work. Probably 4 years solid either collecting or doing field trails. (The gray beards are laughing at me right now. 4 years? Hah!). In any case, many -ologist types do field work and this work brings its own rewards. It generally is hella fun and part of the main attraction of being an -ologist.

The downside is that field work can be dangerous, regardless of where your study site may be. Field work can be even more tricky if you are of the female sort. I encountered enough weirdness during my time in the field that I am reluctant to offhandedly send my trainees out alone.

For example. (I'm cherry picking the most annoying examples -- there were others). Once, while collecting by the side of the road, I was asked to breakfast by a man that looked exactly like this (I am not kidding) and drove a car that looked like this (how can you NOT be a machodouche in a car like that?). He thought maybe I could take a break and we could have a chat at the local IHOP? Um, no thanks. I'll pass on the pancakes and certain death, thankyouverymuch.

Another time I was manhandled by Drunk Joe while ordering dinner at a bar after a long day collecting in a far-off place. All I wanted to do was drink a beer, grab a gigantic hamburger and hole up in my hotel...and random drunk Joe felt the need to massage my shoulders and fiddle with my bra straps. I shrugged him off until my food came...and then I walked in the dark, alone, to my hotel.

I was completely fine both times, and probably extremely lucky. On most occasions out in the field I was alone -- I drove all over a portion of the states by myself, jumped on people's land or hiked into public lands, collected my critters and went back home. And during most trips nothing happened. However, had something happened it would have been really difficult for my kin to have recovered the body since no one knew where I was at any given point. This was probably really stupid.

While I haven't had to face the prospect of getting invited to join the cast of Tarantino's "Death Proof", I've found myself in some interesting situations in the field. Admittedly, I traveled for collecting purposes far more as a grad student than since, but because of what we do and did, I have gone to some unusual places to get the beasts we need - locations where making a mistake can be magnified simply due to the circumstances. Hell, I have even had to carry a gun for science (NTBI represent)!

As one example, I was in the high Arctic one summer camping near a small inlet miles from the small town from which we had embarked. There were four scientists, two guides and a dog. The dog was identified as the "polar bear dog" and it was never clear whether that title was meant as "polar bear distraction snack", "early warning system" or some combination of the two, but the dog clearly wanted nothing to do with the whole affair and bolted as soon as we got to our camp site. Our guides seemed more concerned about losing their neighbor's dog than not having it for the bears, so that night we pitched our tents in the middle of an enormous barren and didn't worry about it. Afterall, the guides were going to stand guard.

The next morning we woke up and got talking with the guide who was awake. We noticed that the top part of our tent was missing, and although it was covered by the fly, we asked about it. "Last time, a bear collapsed the tent and broke it." was the response. Apparently no one was hurt because the bear got startled by the ease with which the tent deflated, but the previous occupants had been understandably startled by giant paws on them in the middle of the night. Hence, the "polar bear dog" (who, BTW, was still MIA).

Slightly unnerved by this news, we were even less enthused when the second guide woke up and had been sleeping in the boat. "Was something wrong with your tent?" we asked. "No, I was scared of bears." was the response. Thanks dude.

In any case, all went well on that trip. No bears were sighted and the dog was eventually found (not much to hide behind 500 miles north of the tree line), but field work that seemed routine at the time has certainly led to tragic endings.

In these situations, bringing trainees can be particularly stressful because rather than being responsible for only myself, I now have to worry about the actions and reactions of those I bring with me. I know that there have certainly been times in my past when I pushed the boundaries of safety for one more sample, for something that looked critical at the time, or even to ensure that everyone else in the group was safe. There is certainly the mentality of "I've come all the way here, spent all that money, and need to make it worth it". Clearly nothing in science is worth bodily injury, but in the right circumstances, apparently mundane decisions can lead to bigger than anticipated consequences. Getting this across to trainees is exceedingly important to me now, though I would not have thought about it that way a few years ago.


I'd like to come up with strategies so that my trainees are not confronted with the same scenarios that I walked myself into. The most simple solution of course is to insist that no one go alone to the field. This doubles the cost of field expeditions, and some field work (like you describe above) is going to be dangerous no matter what. This doesn't mean, I think, that we let our guard down for the expeditions that aren't obviously dangerous. Field work that seems rather safe and benign might not be. I considered carrying a gun at one point, but someone informed me that I would have to be willing to actually use it. Plus, I'm more of the sort that would take forever to root around to find said gun and would then just be the gun supplier for said shady person.

So what are the strategies, or rules that we can impart to people before sending them off on, arguably, the most fun aspect of the job?

The solo student in the field is less of an issue for my people because most of our field work is done in groups in distant places, so it is not the kind of thing where an individual would wander off by themselves. I also would be on the side of "having a gun is more likely to get you hurt than not", but that is a personal view and likely influenced by my gender in no small part. I think it is a fine line between impressing safety concerns on trainees without making them paranoid, since the intent would never be to send them to a place with foreseeable danger. It is also, however, important for the trainee to know that they can voice their discomfort with a situation without being labeled as unwilling to deal with adversity. This is especially true for what we do, because I would rather have someone bail early than panic in the middle of everything and put others at risk. I don't know what the answer is and it may be different from one student to the next. I do know that in several labs I am familiar with, field travel is disproportionately allocated to those who are seen to be dependable and can get shit done. How that relates to the ability of trainees to voice concern for their safety is not clear to me, but I can see where it might have bad consequences.


Right, and I think this is where I want to be particularly careful. I could easily see the scenario of the 'most dependable' or 'most able to get shit done' mutating into 'the easiest to send out' and that person being the dude, given my worries that field work entails another aspect of danger for women. I certainly don't want to perpetuate that kind of inequality. I think some simple things I can do is to insist everyone goes to the field with at least one other person, carries a cell phone and has a working GPS. I might insist on calls both in and out of the field, probably on a daily basis. It would also be good to have people inform park rangers where they are going to be, especially should they be doing off-trail collecting. Other than that? I'm out.

I think those are reasonable requirements and most people will probably augment with any additional precautions that they feel are necessary. Obviously the primary concern is making sure your people are safe, but it is an easy trap to equate safety with least likely (in the PI's view) to be the subject of an attack (in your case) and freak out in adverse conditions (in my case). Judging that a priori is bound to lead to problems.

Maybe we should blog this and let others weigh in?

26 responses so far

Solar Sea Slugs: Part animal, part plant... or not?

Sep 12 2010 Published by under [Biology&Environment]

Original image here.

(Update here)

Sea slugs are far more interesting than their name might imply. Aside from being beautiful, they have some unusual ways of making a living. In the case of a few unrelated species, they steal for a living.

A handful of sea slugs have found away to make the most of the algae they eat. As they take in the cellular contents of the algae, they are able to separate the components and isolate the light harvesting organelles, the plastids. Whereas the majority of the chewed algal is digested, the plastids are spread throughout the specialized digestive track of the slugs so that they form a layer all over the upper part of the slug, giving it a green color. Depending on the species of slug, the animal can then rely entirely on the plastids for weeks to months as the sole source of energy, making them the solar powered slugs.

Elysia chlorotica feed on algae and then steal the plastids to harness solar energy.

But here is where the story gets interesting. It is well documented that plastids have high protein turn-over, especially in their light harvesting complexes. The constant barrage of photons breaks the antenna proteins down and they need to be constantly replaced. Those proteins, however, are not produced by genes encoded on the genome of the plastid. Instead, they are nucleus-encoded and targeted to the plastid by the cell cytosol, thanks to a signature extension on the 5' end of the transcript. Therefore, the algal nucleus is essential for the continued maintenance of functional plastids. But the slugs sequester ONLY the plastids, no nuclei. How do the slugs keep the plastids going for months in the absence of the algal nuclei and the essential plastid proteins they produce?

In 2008, it appeared that there might be an answer. Rumpho et al (2008) looked at the genome of E. chlorotica and identified genes that appeared to be derived from the algal nucleus. Gene transfer from the nucleus of an algal to that of an animal for the purpose of allowing the slug to maintain its own plastids! Needless to say, this story got a lot of press. The only issue was, there were very few genes found, and none of the major antenna proteins one would expect must be there. But it was a PCR-based survey, not a genome sequence, so people reasoned that the genes were there, just not PCR friendly for whatever reason.

Not so fast, claim Wägele et al. in an article released yesterday in Molecular Biology and Evolution. Wägele et al. sequenced cDNA from two slug species made from RNA transcripts (genes being expressed by the animal) extracted from plastid-containing slugs that were kept without a food source, and were thus entirely dependent on the plastids for carbon. Based on the findings of Rumpho et al. (2008), the expectation would be that genes encoded in the slug nucleus that had been transfered there from the alga for the purpose of plastid maintenance would be highly expressed under these conditions. Afterall, the plastids are actively photosynthesizing for the slug and have to deal with the wear and tear of the job.

But contrary to expectation, Wägele et al. found NO evidence of the antenna proteins, the Calvin cycle enzymes or the small subunit of RuBisCO (which is absent from the plastid of the algae the collected slugs were feeding on). This means that the plastids have no back-up proteins - once a protein that can not be made by the plastid breaks down, that's it. Based on what we know about plastids, this should happen within a matter of days - without a constant stream of new proteins from the nucleus, the photosynthetic apparatus should cease to work.

But that is NOT what we observe in the sea slugs. They maintain functional plastids for MONTHS. One explanation is that transcript levels of these critical proteins were too low for detection, but this is an entirely unsatisfying conclusion because 1) Next generation sequencing was used to produce very deep coverage of the transcripts, and 2) the small subunit of RuBisCO alone, accounts for roughly 15% of all transcripts in young plant leaves. The probability of missing all of the transcript necessary for the plastids to survive is virtually nil.

So what is going on? The answer, I'm afraid, is elusive. What we see in nature can not be explained by what we know about the components of the system. The proteins are not being made by the slug and the plastids can not survive as long as they do without replacement proteins, or so our current knowledge would suggest. Something has to give to explain our observations and I'm am eager to see what it is. With the E. chlorotica genome soon to be completed, answers may be on the horizon... or not.

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

Wagele, H., Deusch, O., Handeler, K., Martin, R., Schmitt, V., Christa, G., Pinzger, B., Gould, S., Dagan, T., Klussmann-Kolb, A., & Martin, W. (2010). Transcriptomic evidence that longevity of acquired plastids in the photosynthetic slugs Elysia timida and Plakobrachus ocellatus does not entail lateral transfer of algal nuclear genes Molecular Biology and Evolution DOI: 10.1093/molbev/msq239

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