2009

Refrigerators

Back to the idea of saving energy! The semester is almost over, meaning there is a slight amount of time to breathe and think and take care of little lab chores that have been bugging me. I was reminded of this particular lab chore - cleaning out one of our -20° freezers - by a refrigerator problem at home. We have an in-door water dispenser, and suddenly about two weeks ago it started misbehaving. Every time we open the door, it squirts out ~10mL of water! The current solution is taping a Barberito’s cup to the door, a bit wabi-sabi of me I know. But, I’ve looked underneath, I’ve tried manipulating the cables and lines to the door, I just can’t fix it myself. So, we wait for the repairman, and keep a cup taped to the door that gets emptied into a plant once a day.

It has been bugging me (slightly) for a while that we have two half-full -20° freezers in the equipment hall. We have another one in the lab for primary usage; these are for projects that are active but don’t need everyday access, and then the -80° for longer-term storage of reagents and DNA. That seems a bit of overkill or splitting hairs on the needs of each freezer, and I know that the older freezer could get to temperature within a few hours if we need it again. For now, I’m going to turn it off and save another percentage of lab energy. The greenest lab in the Genetics Department may be a minor distinction, but I’m shooting for it!

No More Sushi for Me

If you check out “EEB & Flow”, I’ve got a new post there on the intersection of DNA barcoding and sushi tuna. When you have to think too hard about whether you should order something off the menu, it probably isn’t worth eating. Darn, I’ll miss sushi though. I wonder if tofu + wasabe tastes okay?

New Salad Spinner

I’m delighted to announce the arrival of a second salad spinner, this one purchased for $2 at Potter’s House, to the lab. We use these - with hot-glued PCR racks inside - as pre-PCR centrifuges. You can buy such things of course, Phenix Research has a small plate centrifuge for about $500 (and my refrigerated plate centrifuge for high-throughput DNA isolation and precipitation cost $15,000), but when all we need to do is get the bubbles out of our PCR mixes, the salad spinner does just fine!

Conservation of Genetics

I’m pleased to see my obsessive relationship with Tajima’s D coming to fruition: my paper will come out in Evolution in the next few months, indicating that despite our tendency to assume a data set is neutral until proven otherwise, the average mitochondrial data set does not behave the way this test of neutrality indicates it should. On the whole, there is a strong bias for negative values of Tajima’s D, suggesting we may need to re-think our nulls in evolutionary biology. However, it makes me nervous to put too much faith in this one analysis of one locus of course! Driving home from Asheville the other day I got very nervous that the effect noted in this paper: what if it is an effect of how researchers curate their data into NCBI? When I got home I checked, and there is a small “curation effect” but I think the biological effect is still strong. Hard to be confident when there are so many factors involved.

In other news, I’ve recognized just what a valuable resource is building up in my -80° freezer: several studies’ worth of DNA isolates, from seastars, isopods, barnacles, fishes, and so on. I’ve had a tendency to try and answer a question (grabbing new samples) and move on; but there is a lot more work to be done on all of those DNA samples. It was hard to get them, they are valuable, right?! So my next rotation student should expect to hear the question: “What do you want to do with all the DNA in my freezer?”

Dirty Times



You’ve probably heard about the incredible mass of plastic in the North Pacific Gyre, it’s estimated to be twice the size of Texas. The video above shows some work going on in the Pacific quantifying the constant migration of small particles of plastic towards this trash dump. Such a shame we can’t figure out a way not only to clean it up, but to recycle it - maybe make our next generation of pipet tips from this plastic?

Things are running smoothly in the Wares lab right now; 3 papers in press that are having their proofs/final edits juggled, and two proposals. That should make for a busy last few months of the year. I’m also pleased to have been invited to contribute to the more-widely-read blog “EEB & FLOW”, so watch for good stuff there as well.

Keeping it Unreal

One of my favorite local cartoonists (his work was shown previously in the “Zombie Semester” entry) is Joe Havasy. A bizarre blend of biology with gory illustration and pop colors is what attracts me to the paintings in my office of a squid catching and squeezing a whale on a brilliant bubbly background. Here, Joe actually makes some of our least attractive study organisms - freshwater mussels - look very cool indeed (as they are!):

Tokyo

I’m off to Tokyo tomorrow as part of a trip to talk as an invited speaker at the Crustacean Society meeting. Part evolution, part ecology, part physiology, and mostly just a lot of love for these beautiful creatures!



I’ve wrapped up two manuscript revisions in the past 2 days, written a lot of verbiage for 3 grant proposals, and done so without much sleep thanks to the flu ravaging my household (having a toddler who drools a lot can’t help). But so these things are, for the time being, DONE. Meaning I can leave and actually turn my machine off. That’s when I noticed how long my Mac Pro had been up, problem-free: 85 days. As long as I’ve owned it. No crashes, at least 3 genome assemblies, web interactions, thousands of emails. We’ve come a long way from the beasts I had to restart several times a day during grad school.

Why Barnacles?

Most people who work with me know I work on barnacles. Of course, I study a lot of things - in the past few years my lab has had projects pertaining to corals, polychaetes, cladocerans, isopods, seastars, fishes, and certainly barnacles (that’s five phyla, plus I was co-author on an Apicomplexan phylogeny paper for six!). But as somebody who is interested in how passively-dispersing larvae interact with the environment, including ocean currents, physiological gradients, competition for space, and so on, barnacles are really a nice choice. They’re hermaphroditic, sessile, fecund, and easy to find. They were the choice taxon of Charles Darwin. They suggest endless questions of morphological plasticity (and stasis!), adaptation, speciation, and biogeography. They keep intertidal rocks from being too slippery to stand on. And, for some at least - I haven’t yet been anywhere that I could do this - they’re really tasty. Of course I am most interested in what the nauplius larvae are doing, and there isn’t much of a meal in things that are less than 500 microns in size, so next time I’m in Chile I guess I better find a market that serves up the adults!



In other news, Penny Haddrill’s work in my backyard (the Five Points Biological Station) has confirmed not only that we have an abundance of D. melanogaster (if only they could outcompete the mosquitoes), but also the recent invader Zaprionus, an attractive but destructive little fly that will apparently be a problem for my peach tree in years to come. If anybody has ideas for some good evolutionary ecology to be done on a backyard that looks wild but is predominantly composed of invasive species, I guess the FPBS is the place to be.

Field Station for Genetics


That’s it. You are looking at the new Five Points Biological Station, a.k.a. my backyard. I’ve collected stream microbial samples from Brooklyn Creek down in the trees at the back. The mown patch is an experiment by a friend of mine who is a landscape architect. Apparently earlier this week the PIRE students came to gasp in awe at the biomass of invasive plant species (kudzu, japanese stiltgrass, honeysuckle, and so on) in my backyard. The pot with rotting bananas in it is there to make collections of Drosophila for Penny Haddrill, who is in town and gave the Genetics seminar last week. I may have to start charging access fees - if you want to use the FPBS you have to sit on the back porch with me and bring some beer so we can enjoy these really nice evenings of late....note the free-ranging carnivore population too - there’s probably a study to be done on her as well.

Nex-Gen Teaching


We have started updating the Evolution teaching lab in a lot of ways this year, so far with really good results. We are sequencing through some mutants for Rifampicin resistance as an addendum to the Luria-Delbrück lab that Kelly Dyer and I added, and so after explaining 454 sequencing (and good ol’ Sanger) to them last week, we squeezed in a field trip to the Georgia Genomics Facility today. Here is Ken Jones, the new Associate Research Scientist, explaining SNP genotyping to the class (sorry, I only got the back of your head, Ken).

Zombie Semester

Well the semester is upon me again - this fall I’m teaching my Evolution Genetics lab course with Kelly Dyer, which is a great change, and the “Welcome” class that we teach (it doesn’t have a good name...it used to be “Professors on Parade” but there were too many easy references to clowns and people in tiny go-carts, it is the class where new students learn what research is going on in the building and are exposed to basic research tools, bibliographic and bioinformatics stuff). So, really a pretty easy load, I’m lucky. And several papers got accepted this month, so I’m now at the point of having more papers published in 2009 than months so far, and more papers published than I am old (I’m really stretching for tenure criteria, can you tell?). I just got the final word on my NSF Bio-Oce proposal, though, and that word is “no” so the semester is - as always - focused on revision and resubmission.

But at the same time, we have a lot of very real concerns. We’ve been told to carefully manage student illness in our classrooms, to help avoid pandemics associated with swine flu. But what I’m really worried about are zombies (unicorn zombie image below from my favorite local artist Joe Havasy) - if you read this paper you’ll see that we could be in very bad trouble indeed if zombies attack!

Concorde Fallacy

It is remarkable how many times the Concorde fallacy is invoked in this job. A lot of work sometimes goes toward projects that you suddenly recognize need to have the plug pulled. Today was the second time in the last year I’ve gotten within two weeks of a proposal deadline and my collaborators and I realized we just didn’t have it all together. Still, some good ideas for collaborative papers emerged from the ashes so it isn’t really “sunk costs”!

The lab is slowly pulling itself back together after our major summer cleaning. It appears that our PCR contamination problem may be associated with the live cultures of crustaceans in the room; at least, whatever it is appears to be airborne contaminant, because we can set up reactions across the hall with the same reagents and pipettors and the reactions are clean. Very strange.

One of many reasons the lab seems so quiet this week is that our summer SUNFIG student, Jesyka Meléndez, has headed home. Despite all the turmoil of the summer, she managed to take a project from basically ground zero all the way up to finding some interesting results about genetic diversity in small populations of the snail Melampus bidentatus on the Georgia coast. When one can go from no research experience to a significant p-value and showing that a species behaves as a metapopulation in less than six weeks, I’d say that person has great potential as a researcher - thanks for your hard work, Jesyka!

Fecundity, Part 2

We can now congratulate Tina Bell on being the second lab member in as many months (it felt like weeks) to successfully defend her Ph.D. She will be doing a postdoc with my (better looking) doppelganger Erik Sotka at College of Charleston, great work Tina!

It has been a hectic past 2 months, obviously, made more hectic by a lab contamination problem that really stymied me. A series of bands, looking almost like a ladder, up to about 300bp that affected all of our mitochondrial COI reactions. We replaced reagents, we tried filter tips, we tried changing reaction conditions, all sorts of things. In the end, it looks like sloppy pipetting put something in our pipettors that is able to aerosolize into reactions. What that “something” is that isn’t exactly COI but responds to those primers, I don’t know. In the meantime, I’ve shut the lab down for a well-needed cleaning and overhaul, including using DNAZap on all items used in PCR, getting rid of lots of junk (apologies to the cleaning staff for all of the very full trash cans, and no most of it could not be recycled - what could be passed along to other labs was, however), and so on. We’ll be a little leaner and meaner now; with fewer students perhaps I’ll sleep a little better at night, too.

Speaking of the conservation side of the lab (the recycling, not the getting rid of students), I’d previously detailed (on my pirate-hacked wiki that I had to shut down) the work we’ve done in the lab to cut down on energy use, and as of late May 2009 our efforts had cut our kWh usage by plug-in gizmos by well over 10%. With the recent overhaul of the lab (and reduced population size), I’ve decommissioned another older G4 (though that was thanks to getting a new Mac Pro, so no net savings) and we’re replacing a 9-year-old Dell Workstation with the Mac Mini for gel doc and Nanodrop runs. That should cut the power consumption in half for that computer station, though I doubt it will dramatically improve my Hirsch-Index-per-kWh numbers!

Submission

Funny all the ways that “submission” gets used. Seems appropriate to assume the submissive posture as I submitted an NSF proposal and a manuscript to Journal of Biogeography today. The new “news” website is almost up and will be more hacker proof (darned wiki!) which may keep me more sane (or less bald) in years to come.

Fecundity

It looks like the Wares Lab has finished up its first Ph.D. - Scott Small defended his dissertation last week! We’ve got a few revisions left, but congratulations to Scott - he did a fantastic job over the last few years and I’m looking forward to the 10 papers we’ll get out of this dissertation!

First Blog Stuff: A Green Lab

April 6, 2009
The unexamined conservation genetics lab is not worth leading. It's time to start thinking about the footprint of science, especially in labs that ostensibly are working toward conservation and an appreciation of the processes that generate and maintain biodiversity. I've brought my
Kill-A-Watt into work to start evaluating ways to make my lab more efficient, with a smaller carbon footprint. I pay for carbon offsets, but that is just a financial trick to help me sleep at night (it doesn't work very well; I'm an insomniac!). This week I'm starting with the old chromatography refrigerator I inherited when I took over the lab. These giant glass-doored refrigerators can be useful, but we aren't running allozymes or SSCP gels in there, and really it may be that we don't need the thing at all. I've got it hooked into the Kill-A-Watt and will report on its cost (in dollars and in carbon molecules) soon. My goal is to reduce the kWh of my lab by 10% this month...I'm not sure if that is possible, so let's start crunching numbers. I'm working on the ballpark rate assumption of $0.10 per kWh, which may be a little high for Georgia but keeps the math easy (my friend Jason in Engineering Outreach tells me now that UGA's cost per kWh is $0.065).
Given that, after 24 hours that old chromo fridge used 5.49 kWh - about
1/100 of a typical monthly household energy use. That is actually surprisingly low, I think - that means it would probably cost about $197 a year to just leave it on. It isn't like there is an entire graduate fellowship lurking in that outlet. But, of course, add these things up across campus, or just across a lab...and that is a few pounds of CO2 (about 1.7 lbs CO2-equivalent per kWh). Now I'm going to check out my 'tip incubator', an old drying oven that we use just to make sure our pipet tips are dry - but that sits around heating the air ever so slightly, constantly. More on that tomorrow.

April 7, 2009
Okay, the incubator/oven set at lowest temperature point (holding at 29° in a lab that is probably about 24° ambient) - looks like that costs $28/year, about a sixth of the chromatography fridge (for a much smaller gizmo, that is also not really necessary for my lab). To establish some benchmarks for energy reduction, I guess I need to estimate kWh for a given time period, large enough to tell differences among the gizmos. The fridge used 5.49kWh in just over 24 hours, or about 2000kWh in a year. The oven on the other hand will use about 260kWh in a year (I didn't leave the K-a-W on for very long, so this is obviously ballpark).
A nice reference will be the one thing that I *know* I need for productivity from my lab - my computer. I have a Mac G5 with an LCD monitor, both about 4 years old. They are plugged into an uninterruptable power supply (UPS - fortunately, so I didn't have to shut anything down to plug in the K-a-W). We'll see just how much damage this setup does (to the environment, I mean - my eyes and wrists are certainly getting tired).

April 8, 2009
3.44kWh so far on my computer, in 16 hours. That is dismaying. For all intents and purposes it is almost equivalent to that giant refrigerator, despite having an LCD monitor that shuts off all night. But the computer doesn't - it is often running processes (number-crunching), or I access it from home, and for a few other reasons I leave it on for weeks at a time. There are certainly plenty of scheduling scripts that could be set up to shut it down each night, at least for a few hours, but I'm not sure that wouldn't mess with my (admittedly not high) productivity. I'm going to leave the K-a-W on for another day so it picks up a full day of me working on figures for the
Notochthamalus paper, playing Guest Editor for Estuaries & Coasts, and of course checking si.com for Braves stories.
The trade-off may be that my lab currently has 8 computers - more than one per student. A couple are devoted to tasks, like the Gel Doc machine that is a real clunker. So I can't get rid of those, but that one in particular could be put on a
shut-down schedule (except it is Windows, so that probably wouldn't work...). And another old machine is only serving information, that function could be transferred to another machine. Lots of options, for now I'll just keep crunching numbers.
Update: I found a python script that was able to rip the MySQL data from the old server G4 into HTML format. This is really dry reading for you, but I know someday at least *I* may find it useful. Anyway, the old G4 and its monitor are now shut down and unplugged from the wall, and I can access all that info (even with pictures) here on my main desktop. If you take nothing else away from reading this wiki-blog, its that learning scripting languages like perl and python is really, really useful in this information age. So, I'm going to assume that whatever kWh load (about 1980 kWh/year) my G5 puts on the world, I just saved by (hopefully permanently) unplugging my 9-year-old G4.

April 13, 2009
The weather outside is gloomy, but through the fog - is that the Flying Spaghetti Monster? No, just a Monday looming. Final acceptance on Clare Scott's honors thesis came today, it is now "in press" at Ecology of Freshwater Fishes, good work Clare! This time of year seems to be manuscript-juggling: two dissertations, our paper at MEPS, a project starting up for J. Biogeog., and two Estuaries & Coasts manuscripts in revision. That means I need to be reminded every five minutes which project I'm working on.
As for the Kill-A-Watt, the most recent info comes from my printer - which is a Lexmark that can print on both sides, so already a green step-up from our older laser printer. After 20 hours it had consumed 0.4 kWh, costing about $20/year to just leave it on. Certainly I could imagine figuring out a way to put it on a kill switch at night though, could cut that price in half. I'll add up those things later on in this project. The other thing that I measured over the weekend was my bank of MJ thermal cyclers. Obviously these are the bread-and-butter of the lab, so their usage is not really that negotiable. But, sadly, their job is to cycle back and forth between heating things and cooling things well past ambient, and they aren't insulated (they need to be able to change temperature rapidly, after all). So, 3 thermal cyclers under more-or-less normal usage for 94 hours used 8.32 kWh...about 775 kWh a year at a cost of about $77 (by my $0.10 guesstimate, which is a bit high - see post from a few days ago - but keeps math easy).
Now we are starting to get into the not-negotiable power consumption. For one, my ultracold freezer. That is necessary for long-term storage of valuable (hard to get again) DNA samples, and some enzymes. It churns pretty much constantly to keep the interior of the freezer at -80°C, and it is big - about 480L interior volume, and that is about 80% full (probably could be cleaned out and be 50% full). It runs 220V so I can't use the K-a-W, but online estimates from manufacturers suggest it is going to use 16.3 kWh
per day, or about 6000kWh/year. Obviously these ultracolds are a big part of our footprint. The only way I can think of, off the bat, to deal with this is that there is a "departmental emergency" freezer in the same hall, that is almost empty and also running at -80°C. Maybe we need to negotiate a different arrangement? But, then, we've all had to deal with the crisis of a freezer that needs repair. At that time you need to move your irreplaceable samples immediately so they don't thaw, and so probably cannot wait for a freezer to get to temperature. At least, that is our fear talking...
SO the current tally: chromo fridge (now unplugged), incubator (now unplugged), G5, G4 (now unplugged), printer, ultracold, thermalcyclers used about 13000kWh/year. By unplugging the unnecessary stuff (for now), I'm helping...but there are a lot of gizmos to go. Assume the other 6 computers in the lab are also about 1800kWh/year - that is 10800kWh/year, a pretty massive load. So how do we cut back on computer load, without affecting computational power and analytical needs? That's the next thing to tackle. It will be, uh, a little easier once my two students finish up this summer...another G4 can be retired, for sure. But it is also important to figure out how some of these machines can be put on SHUTDOWN schedules, while still maintaining appropriate access to some data/servers at night.
Also, I sent this email today:
To whom it may concern,
every week I receive an issue of Columns, specifically addressed to me. I do find the information in Columns of value when I have time to read it, but I've noticed that dozens of copies in my building alone are immediately recycled or thrown away. Would it be possible for the University community to receive Columns as a formatted HTML email? Or to unsubscribe from the paper copy if they do not intend to read it? I notice in addition to the copies placed in each of our mailboxes (addressed to us, so our staff takes the time to sort them into mailboxes), there is a rack with extra copies in our mailroom.
At a time when the University is facing enormous financial burdens, changing the delivery default of Columns could be an enormous financial turnaround, not to mention an environmental shift that is in line with President Adams' stated goals. I'll look forward to your thoughts on this matter.
cheers John

There are lots of stones left to turn over at this University. If you are interested, check out
http://gogreen.uga.edu/

April 16, 2009
Monitors are a big part of the power suckage of computers, but I'm surprised it isn't worse. I hooked the K-a-W up to the 24" LCD on our Mac Pro for a couple of days; looks like it is responsible for about 260kWh/year, or about $26 in operating costs (and about 445 lbs CO2e). So that leaves me pondering why
the computer itself is so power-hungry at night? Well, it isn't set to go to sleep. So, whether I'm typing on it or not is immaterial. But I hesitate to set it to actually go to sleep, since that can grind analysis to a halt (this week for example I had a long PAML run and a long IMa run going; plus, I contact my G5 from home on occasion). There are ways to script a UNIX-based machine (like Mac OS) to check its processor load before going to sleep, but I'll need to do more research before applying this to my machine (for one, that link is 7 years old - OS X has changed a bit!). There are funny solutions to this problem, including the application Jiggler, which apparently mimics the mouse being jiggled often enough that the system won't go to sleep. This seems to be more for people who can't control the sleep/no sleep function, i.e. they aren't administrators. I had this problem with a Windoze machine while at UNM, I could *not* get it to stop going to sleep during a long analysis - so I put its mouse on a shaker table!
Anyway the trick for some of our machines may be to tell them explicitly to go to sleep - and warn folks not to use those machines for extensive analysis. The trick is, as haphazard as some of the development of my lab has been, it is hard to make major cuts without more control over the
environment of the lab. Can't control the heat/air. The fume hood is OFF about 99.99% of the time because we don't use nasty chemicals - we just culture algae under a gro-lite in there. That's good because constantly-running fume hoods have to move so much air, they can be as energetically expensive as three U.S. households!
What I've cut so far - about 4500kWh/year - is about 7500 pounds of CO2 equivalent each year, and about $450. If you don't count heating and cooling but just the stuff we plug in, there is still another 12000 (computers), 6000 (ultracold), 6000 (other freezers and refrigerators), and probably another 6000 overall in other gizmos, or about 30,000kWh/year of energy use. So, for now I've met the 10% goal in a very coarse way. Many of us are able to ride our bikes in most days (I ride in at least 300 days a year)...more later...

April 20, 2009
As Earth Day approaches, continuing the energy-saving theme of this page seems good. At one faculty retreat a couple years ago, we began to discuss ways in which our department or building could reduce our footprint a bit. One thing that came up was a rant against using the elevator - at least, if you are reasonably healthy and not going too far or carrying too much, right? Well, I just came across
this post that explains that elevators are one of your smaller concerns in a day's business. On to the next problem.
For now I'm leaving aside the consumption of kilowatt-hours by my lab; most remaining gizmos are somewhat necessary or infrequently used (and off/unplugged). The waste stream is probably the next good place to start. We try to maintain a very low-toxicity lab: no ethidium bromide (we use
GelRed for staining gels), no radiation, extremely infrequent use of polyacrylamide or TEMED, and so on. Probably about 90% of our chemical usage is water, common salts, and naturally-derived enzymes in small volume. Our chemical usage could still be tweaked, but by and large mostly benign.
Plastics bugs me. Lots of virgin polypropylene. I estimated about a year ago, based on purchasing for the lab, that the common yellow tips used on 20µl and 200µl pipettors added up to about 4kg a year - the equivalent of 420 20-ounce soda bottles (at 28g each). Given the
soda consumption of people in my lab (I'm just as guilty), I suspect we also drink and recycle about that many bottles a year. Which is worse? Washing and reusing the tips would definitely take a cut into our productivity (and would probably cause my students to mutiny), and recycling them is almost impossible (I think polypropylene is #5 plastic, which is not easily recyclable - and of course even if we think that our tips are only touching benign substances, would you buy a teething ring for your kid that advertised it was made of recycled scientific labware?). But, then, cutting out soda might put a notch in our productivity too, given the admitted caffeine addiction we've all got.
Wow, I didn't solve any problems with this information - bummer.

May 15, 2009
Wow, the end of a long semester and the beginning of summer. It is good to have a bit more leisure to consider how my projects are doing; just had my (almost) global phylogeny study on
Chthamalus published in PLoS ONE, and today finishing up revisions on a Mark Vellend-inspired paper on genetic diversity in the Georgia Coastal Ecosystems domain.
I'm continuing the assault on electricity usage by my lab; right now our temperature-controlled room is not harboring any experiments or anything living (intentionally). Usually this 200-square-foot space is cooled to 18°C; it usually breaks about once a year because of the load of the first really hot days on the cooling system. If we aren't using the space, why not turn it off? That's gotta be worth something.
The question is, how does this energy usage affect the science? One could argue that my scientific program hasn't expanded to fill the resources I had available, or that I can only cut back in inverse proportion to my productivity. Only time will tell! We may have to devise a metric for productivity per kWh, perhaps the
Hirsch index per kWh? Right now I'd be at about 0.00043 - no matter how it compares with others, that is a pretty unimpressive looking stat. I better get back to work.