The “underwater view” will haunt my dreams. Lampreys really, really hate the smell of rotting flesh.
It comes in pints! The new Sam Adams Boston Lager Glass (TM) may not be the paragon of beer-containment that it claims, but it is the latest in a long history of cups, beakers, and tankards.
Defining a new adaptive zone for evolutionary ecology. The observation that anoles living in different micro-habitats had different body types, and that those body types might be related to life in the micro-habitats, was first published fifty years ago.
That burbling sound is “Thus Spake Zarathustra” playing underwater. Now dolphins are using conch shells as tools.
Finally, from a compilation of timelapse videos of plants, here’s climbing morning glory. Tropisms in action!
Yes, I’ve actually kept busy enough this week to make it all the way to Friday without compiling the weekly linkfest. So, er, here’s the best thing not related to next-generation sequencing I did manage to see all week: Julia Child explaining the Miller-Urey experiment, then making her own “primordial soup.”
Video via Ferris Jabr. That original experiment turned out to be more successful than originally known. ◼
The future is in the cloud? Photo by Extra Medium.
Biologists are about to have access to all the genetic data we could ever want. Unfortunately, once we have that data, we have to figure out where to put it—and some way to sift out the bits that answer the questions we want to answer.
That’s the first day of the NESCent workshop in next-generation sequencing methods in a nutshell.
Brian O’Connor, who gave the morning lectures, framed the immediate future of biology as a race between technologies for collecting genetic sequence data and technologies for storing and analyzing that data. Moore’s Law is that computer processor speed (really, the number of transistors packed into a single processor chip) doubles about every two years; Kryder’s Law is that computer storage capacity roughly quadruples in the same amount of time. But in the last few years, and for the foreseeable future, DNA sequence collection capacities are growing on the order of ten times every couple years.
In other words, there may very well come a day when the cost of storing and using a genome (or genomes!) belonging your favorite study organism will exceed the cost of obtaining those data.
O’Connor suggests that one major way to stave off the point where computing capacity limits data collection and analysis will be to use more “cloud” systems—remote servers and storage. Lots of institutions have their own servers and computing clusters. I’m already working with data sets too big to carry, much less process, on my laptop; I filter out the subset of sites I want on the server where the data is stored, and download (some) of that smaller data set for local work.
However, high-capacity computing facilities need a lot of lead time, and infrastructure investment, to scale up. That isn’t practical for individual projects. In such situations, and for researchers at institutions that don’t have their own high-capacity computing resources, commercial services may become a major alternative.
In the afternoon, we got started with one such alternative, Amazon EC2, or “elastic cloud computing.” Yes, that’s Amazon as in Amazon.com, the place where you buy used textbooks. It’s possible to rent processing capacity and storage from Amazon, and the services are provided in such a way that when you need more, you can just request it. “Instances” running on Amazon’s computing facilities can run Unix or Windows—you can interact with an instance via a remote desktop-type interface such as NoMachine’s NX system—and will run any program you’d care to have chew its way through your data.
All of this, of course, assumes you have the budget. It’s not clear to me how easy it’d be to estimate computing needs ahead of time for grant-writing purposes; but on the other hand, you can probably expect that whatever estimate you come up with will likely go that much further when you finally start working a year later. Over beer at the end of the day, Karen Cranston, the Informatics Project Manager for NESCent, told me that Amazon’s pricing is close enough to that of the high-capacity computing facility at Duke University that it’s often worthwhile to use EC2 for short-term, high-volume projects simply because it’s so quick and easy to bring new resources to bear.
As a not-yet faculty member, the cloud means I can plan to do genome-scale work even if I end up at an institution without the on-campus resources to build its own cluster. That’s potentially pretty liberating. ◼
Sighted in the woods near Northgate Park, Durham. For real. Photo by jby.
I’m spending the next two weeks in Durham, North Carolina, for the NESCent workshop on next-generation sequencing. Which is to say, a workshop about collecting great big genetic datasets, and what you can do with them once you have them. I’ll be stretching my programming skills to the maximum, and hopefully getting a head start on some ideas I’ve had for good old Medicago truncatula.
If time permits, I may take a page from Carl Boettinger’s literally open lab notebook and post some notes and thoughts here as the workshop progresses, but it’s looking likely to be a full two weeks, and time may very well not permit. ◼
Is that a tennis ball in your pocket, or asymmetric hypertrophy of your iliopsoas? Oh. It’s a tennis ball. Photo by Steve9091.
Quick, tell Coach Schtitt to change up the drills. Something about the athletic demands of tennis leads high-level players to develop asymmetric bums.
Nothing revolutionary comes easy. Engineering grain plants that can host nitrogen-fixing bacteria would be an historic breakthrough for agriculture, but it won’t be simple.
Try not to forget. Memory really doesn’t work the way most people think it does, in a lot of important ways.
Like my relationship status with “food miles.” Even when you do the math, figuring out what lifestyle choices are most sustainable is complicated.
So, I’ve known for some time that On the Media co-host Brooke Gladstone has a new book out, and that it’s a meditation on media in quirky graphic-novel form, but I didn’t really know I needed to read it until I saw this trailer. ◼
A honeybee explores the depths of a dandelion, one of the species used in Fründ et al.‘s experiments. Photo by je-sa.
If you’ve ever stopped to admire morning glory flowers opening first thing in the morning, then noticed they’ve closed by evening, you’re at least dimly aware of one of the longest-established ideas in plant biology: that flowers open and close on a reliable daily schedule. Different species are open at different times of day, of course, but each flowering plant has its preferred open period, and it sticks to that schedule during its flowering season.
This idea led Carolus Linneaus, the father of modern biological taxonomy, to propose an Horologium florae, or “floral clock” using plantings of species with known flowering times to mark the hours. You can find his table of proposed species in the online version of Linneaus’ 1783 treatise Philosophia Botanica, if you’re not averse to Latin. Studies of flowers’ daily schedules go back to well before English was the language of international science, and continue to the present day [$a].
Yet no one seems to have spent much time considering how flowers’ schedules might respond to the activity of their very reason for being: pollinators. Flowers don’t open just to be open in a particular kind of sunlight—they’re open to attract animals that can carry pollen to another plant, and maybe leave some, too. If a flower receives enough pollen to make seeds by noon, why would it stay open until two o’clock?
According to some new experimental results, the answer to that question is that they don’t [$a].
Jochen Fründ, Carsten F. Dormann, and Teja Tscharntke set out to see whether a selection of European wildflowers adjusted their opening schedules in response to pollination, with two major experiments and a broader-scale observation project. The experiments address whether pollinator activity could change flowers’ schedules; the observations help determine how important those changes might be in studies of plant-pollinator interaction.
A floral clock in Geneva—not quite what Linneaus had in mind. Photo by aranmanoth.
In the first experiment, the team planted wildflowers—Crespis capillaris, a close relative of common dandelions—in experimental plots spaced across a field. Plots were either caged or left open to insect visitors, and Fründ et al introduced bees into some of the caged plots. So some plots had a controlled set of pollinators, some had none at all, and some had whatever pollinators were already active in the field.
The team then watched the flowers’ daily opening and closing in the experimental plots. (They had a lot of help—a long list of names in the paper’s Acknowledgements section ends with “and many others.”) Over the same period of time, flowers in the un-caged plots received more insect visitors than flowers in either other treatment, and had mostly closed by midafternoon; flowers in the caged plots with bees introduced received fewer visitors and closed hours later; and flowers in the plots with no pollinators at all stayed open till evening.
So flowers experiencing the same daylight pattern closed earlier if they received more pollinator visits. The team followed up this result by hand-pollinating flowers of C. capillaris and a handful of closely related species growing in the same field, including dandelions—and flowers of three out of four species closed more rapidly when hand pollinated. Dandelions didn’t respond to hand pollination, a result the authors explain by noting that dandelions often self-pollinate, and so don’t need to wait for animal pollinators.
Finally, the team compiled observations of plant-pollinator interactions from sites similar to their study field located across Germany, and divided them into observations taken before solar noon, when the focal flower species from the experiments above tend to be open, and after solar noon. Which pollinator species visited which flowering plants depended significantly on when the observations were made—to the extent that the apparent importance of C. capillaris and its relatives is entirely different before and after noon.
Of course, these results apply directly to only a handful of species representing a particular group of flowering plants—but it’s a group with a lot of widespread and abundant members, and the result is straightforward and striking. Animal-pollinated plants may not behave much like clocks at all. Instead, they’re more like the patrons of a singles bar: they show up at about the same time and hang around until they find someone to buy them a drink. That’s a dynamic worth keeping in mind for studies of plant-pollinator interaction, since it suggests that the partners a pollinator chooses will depend, at least in part, on whether or not it’s out after closing time. ◼
References
Ewusie, J., & Quaye, E. (1977). Diurnal periodicity in some common flowers. New Phytologist, 78 (2), 479-485 DOI: 10.1111/j.1469-8137.1977.tb04854.x
Fründ, J., Dormann, C., & Tscharntke, T. (2011). Linné’s floral clock is slow without pollinators – flower closure and plant-pollinator interaction webs. Ecology Letters DOI: 10.1111/j.1461-0248.2011.01654.x
von Hase, A., Cowling, R., & Ellis, A. (2005). Petal movement in cape wildflowers protects pollen from exposure to moisture Plant Ecology, 184 (1), 75-87 DOI: 10.1007/s11258-005-9053-8
The annual meeting of the Ecological Society of America is underway in Austin, Texas, this week. If, like me, you’re not anywhere near Austin, do not despair. There are people who will use the Internet to tell you what is going on at the meetings anyway, out of sheer enthusiasm for ecology! Here are the ones I’m following:
So one major credit rating agency has announced it has a bad feeling about the long-term value of U.S. government debt. Whatever could our government—which is to say, we, the U.S. public—have done to warrant that? How about refusing to collect revenue that could pay down existing debt:
Sure, government spending increases debt, and the U.S. government spends money to do lots of things I’d be happy to stop doing. But government does lots of things that any sane person agrees are necessary—paying for police and firefighters, building roads, preventing people from pissing in my drinking water—and even if we cut all those basic services to zero, we still wouldn’t have a balanced budget. (Non-defense discretionary spending for 2010 ≈ $530 billion; 2010 federal budget deficit ≈ $1,294 billion. Everyone can agree that 530 is not larger than 1,294 … right?)
When the government borrows, it borrows against tax revenue that it could, theoretically, collect to pay off the debt. Our collective decisions as U.S. citizens, expressed via elections—with admittedly varying degrees of accuracy and wisdom—have run up historically high national debt while driving the proportion of national income collected as taxes to a historical low. If you were loaning more and more money to a friend who kept working fewer and fewer hours a week, wouldn’t you start to get a bit edgy?
And if all this sounds a bit abstract, here’s a nice concrete number: the increased cost of U.S. debt associated with that credit rating agency’s bad feeling comes to about $322 per U.S. citizen. If I’m not mistaken, that’s a pretty big chunk of the refund I got back when the last round of big tax cuts took effect, ten years ago—and it’s just the start. ◼
You must admit, it doesn’t look comfortable. Photo by Soller Photo.
A movable feast. The neurochemical explanation for those viral videos of dancing squid sushi.
Or, you know, don’t fragment the habitats. To offset the effects of habitat fragmentation and help natural populations adapt to changing climate, just add gene flow.
Coming soon: age-defying low-iodine diets. Axolotls are neotenic salamanders, meaning they become sexually mature without developing the “adult” characteristics other salamander species typically have—unless you dose them with iodine.
Reviving, not revived. After being fished nearly to extinction, the Atlantic cod population—and rockfish, and haddock—may finally be reviving.
We traded guts for brains. Compared to other mammals, humans have unusually big brains for our body size, which means that we also have rather odd bodies.
And we’re not talking about “Tag” body spray. The African crested rat deters predators by slathering itself in poison.
These congratulations will not be withdrawn later. Retraction Watch completed its first year of following up on post-publication reviews and refutations this week—well done!
Beerquake. Photo by dongga BS.
