Category Archives: blogrolling

The Molecular Ecologist: Storing and protecting your NGS data

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Data Barnacles. Photo by UWW ResNet.

This week at The Molecular Ecologist, Mark Christie shares some tips for how to take care of that massive genetic dataset that’s just come off the high-throughput sequencer:

Congratulations! You have recently received a file path to retrieve your hard-earned next-generation sequencing data. You quickly transfer the files to the computing cluster you work on or perhaps, if you only have a few lanes of data, to your own computer. But before you begin messing around with your data, you quickly realize that you should come up with a plan to back up and store unadulterated versions of your files.

For a nice set of recommendations with some step-by-step instructions, go read the whole thing.◼

Nothing in Biology Makes Sense: Making sense of the missing human baculum

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Walruses on the corner If you think those tusks are impressive, you ain’t seen nothing yet. Photo by Joe King.

Over at Nothing in Biology Makes Sense! Sarah Hird discovers a case in which Creationists are willing to cite phylogenetic context to make a point, and that point is that God made Eve from the bone in Adam’s penis. What, you didn’t know that most mammals have a penis bone?

Baculum is the technical term for the penis bone. Many mammals have one – presumably to aid in sexual intercourse. For mammals that mate infrequently, prolonged intercourse ups the chances that a particular male sires some babies. For mammals that must mate quickly, the baculum provides immediate rigidity. And for all mammals, keeping the urethra straight while copulating is imperative, so maybe it’s there to prevent a kink in the works, so to speak.

To see the full phylogenetic context of the baculum, and learn some possible reasons why a male walrus has a two-footer but humans have none at all, go read the whole thing.◼

The Molecular Ecologist: Climate’s a-changin’. Will the living world evolve to cope?

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Warm Fire It’s getting hot out there. Photo by Kaibab National Forest.

Over at The Molecular Ecologist, I discuss a new study that uses phylogenetic estimates for 17 families of vertebrates to estimate how rapidly those animals have evolved in response to past climate change, and compares those estimates to how fast they’ll need to evolve to keep up with projected climate change. Spoiler alert: past rates of adaptation to climate aren’t anywhere near fast enough.

To keep up with projected climate change, Quintero and Wiens estimated that the species in their dataset would have to undergo adaptive change at from 10,000 to 100,000 times faster than the rates estimated in their evolutionary past.

Well, but maybe. To learn whether the data are telling us what the study’s authors say they’re telling us, go read the whole thing.◼

Nothing in Biology Makes Sense: Pseudoscience in scientific clothing

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A snake in the literature? Photo via Wikimedia Commons.

This week at Nothing in Biology Makes Sense!, guest contributor Chris Smith finds something a bit odd in his Google Scholar results:

I recently gave a lecture on the Miller-Urey experiment, and I wanted to pull up the original citation. So, glancing at the clock to make sure I still had five minutes before showtime, I headed over to Google Scholar and entered in the search terms “Miller Urey.” When I started browsing the results I was surprised to find, on the first page, a link to an article titled “Why the Miller–Urey research argues against abiogenesis” published in The Journal of Creation, a product of Creation Ministries International.

To learn what Chris thinks is going on—and how it resembles a phenomenon in evolutionary biology—go read the whole thing.◼

The Molecular Ecologist: Relentless Evolution

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Medium Ground-Finch (Geospiza fortis) Darwin’s finches, like this medium ground finch, are a prime example of what John Thompson calls “relentless evolution.” Photo by David Cook Wildlife Photography.

When I was just starting graduate school, one of the first things I wanted was readings to get me up to speed on the current state of research on the evolution of interactions between species. My dissertation advisor handed me The Geographic Mosaic of Coevolution, by John Thompson (who, it should be said, had been my advisor’s postdoctoral mentor). Thompson turned out to be just the author for the job, wrangling a huge body of research into a clear, straightforward text, and all in support of his argument that metapopulation dynamics—populations linked by migration across a landscape of varied environments—are the engine driving much of evolution.

Now, Thompson’s published a new book, titled Relentless Evolution, which pretty much picks up where The Geographic Mosaic left off. And I’ve reviewed it for The Molecular Ecologist.

Gould’s “paradox of the visibly irrelevent” holds that, if we are to understand the river of evolutionary history, we must look below the spume and spray of year-to-year adaptative change to find the deeper currents that can, over time, carve canyons. In his new book Relentless Evolution (University of Chicago Press, $35.00 in paperback), John N. Thompson makes the opposing argument with gusto: To Thompson, studying the roiling eddies that Gould dimissed as transient and superficial is the only way to understand the deeper currents, and the river’s course ahead of us.

Should you run out and buy a copy? If you’re even slightly on the fence, I suggest you go read my whole review.◼

Nothing in Biology Makes Sense: Science and morality

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NDU stained glass detail Photo by jhritz.

Over at Nothing in Biology Makes Sense, Amy Dapper takes a look at a new study suggesting that thinking about science might promote moral behavior.

In all four experiments, the authors found exposure to scientific thinking led to more moral behaviors. Study participants that were exposed to the scientific priming (or in the first experiment, that had greater previous exposure to science) reported date rape as being more wrong, were more likely to report that they would participate in prosocial behaviors and divided the $5 more evenly between themselves and the anonymous participant.

Of course, I’m flabbergasted by these results, because all of the scientists I know are selfish, amoral hedonists—that’s why we’re all clamoring for cushy, overpaid jobs on the tenure track. But maybe you should go read the whole thing and see what you think.◼

The Molecular Ecologist: Using R to model the spatial distributions of species

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Environmental variation across the range of Joshua tree. Image via The Molecular Ecologist.

This week at The Molecular Ecologist, I’m showing how to use the popular open-source statistical programming language R to estimate species distribution models.

Species distribution models (SDMs) are handy any time you want to extrapolate where a species might be based on where you know it actually is. Maybe you’re trying to figure out where would be fruitful to do more sampling; maybe you want to know where your favorite critters probably lived back during the last ice age; maybe you want to know what regions will be suitable for your favorite critters after another century of global climate change.

Given how widely useful SDMs are, it’s very nice to be able to estimate them using multiple methods implemented within a single open-source framework. To get a taste of the capabilities provided by R and a select set of add-on packages, go read the whole thing.◼

Carnival of Evolution, April 2013

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Tomorrowland at Dusk What kind of sequencing capacity do they have in Tomorrowland? Photo by Big DumpTruck.

The April 2013 edition of the Carnival of Evolution is online over at Synthetic Daisies. This issue of the monthly collection of online writing about all things evolution-y is organized around the theme of the future of evolution—which looks to be full of exciting possibilities. There’s experimental phylogenetics and speculation about radio-sensing animals and species coming back from the dead, so maybe you should go peruse the whole thing.◼

Nothing in Biology Makes Sense: Making sense of pollinators’ role in creating new plant species

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Joshua tree flower closeup A Joshua tree flower. Photo by jby.

Over at Nothing in Biology Makes Sense! I’ve got a new post discussing freshly published results from my dissertation research on Joshua trees and their pollinators. I don’t have to tell you why Joshua trees are interesting, do I?

Joshua trees are pollinated by yucca moths, which are unusually focused, as pollinators go. Your average honeybee will blunder around in a flower, scooping up pollen and drinking nectar, and maybe accidentally pollinate the flower in the process. A yucca moth, on the other hand, gathers up a nice, tidy bundle of pollen in specialized mouthparts, carries it to another Joshua tree flower, and deliberately packs it into place. She does that because the fertilized flower provides more than a little nectar for her—she’s laid her eggs inside the fertilized flower, and when they hatch her offspring will eat some of the seeds developing inside it.

That’s pretty cool in its own right. But what’s especially interesting about Joshua trees, from an evolutionary perspective, is that they’re pollinated by two different moth species. And it turns out that the flowers of Joshua trees associated with the different moth species also look pretty different. The most dramatically different feature is in the length of the stylar canal in the pistil, the part of the flower that determines how the moths lay their eggs.

In the latest development, my collaborators and I tested for genetic evidence that Joshua trees pollinated by different moth species are isolated from each other. To learn what we found, go read the whole thing.◼