Category Archives: science

The Molecular Ecologist: The 2014 Next-Generation Sequencing Field Guide

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Alineando secuencias (1) Photo by Shaury.

One of the most popular items at The Molecular Ecologist isn’t a blog post—it’s Travis Glenn’s “Field Guide” to the capabilities and costs of the many next-generation sequencing technologies currently available. Today we’re pleased to release the 2014 update to the Guide, this time with some new personal insight from Travis in the form of both an introductory blog post and a new table rating the overall quality of each technology:

Overall, if you are in the market for a next generation DNA sequencer in early 2014, the data indicate one clear inexorable trend – think Illumina. For fans of the Brady Bunch – Illumina, Illumina, Illumina! For fans of Star Trek – Prepare to be assimilated by one of Illumina’s Borg-like cubes. For fans of Henry Ford – You can have any NSG instrument you want, so long as it’s an Illumina.

Travis’s post is well worth reading in full, and you’ll want to update your bookmarks to the new comparison tables.◼

One of these moths is not like the other … but does that matter to Joshua trees?

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A Joshua tree flower, up close
A Joshua tree flower, up close

Cross-posted from Nothing in Biology Makes Sense!

A huge diversity of flowering plants rely on animals to carry pollen from one flower to another, ensuring healthy, more genetically diverse offpsring. These animal-pollinated species are in a somewhat unique position, from an evolutionary perspective: they can become reproductively isolated, and form new species, as a result of evolutionary or ecological change in an entirely different species.

Evolutionary biologists have had good reason to think that pollinators often play a role in the formation of new plant species since at least the middle of the 20th century, when Verne Grant observed that animal-pollinated plant species are more likely to differ in their floral characteristics than plants that move pollen around via wind. More recently, biologists have gone as far as to dissect the genetic basis of traits that determine which pollinator species are attracted to a flower—and thus, which flowers can trade pollen.

However, while it’s very well established that pollinators can maintain isolation between plant populations, we have much less evidence that interactions with pollinators help to create that isolation in the first place. One likely candidate for such pollinator-mediated speciation is Joshua tree, the iconic plant of the Mojave Desert.

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Science online, gold-star creationist edition

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Tomatoes You might want to plant your own tomatoes, this year. Photo by rachelandrew.

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Nothing in Biology Makes Sense: Can a creationist be a (public university) biology lecturer?

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2010.02.15 - Life Sciences South The Life Sciences building at the University of Idaho. Photo by jby.

Over at Nothing in Biology Makes Sense! I’m confronting my discovery that the University of Idaho, where I received my Ph.D., has hired an outspoken proponent of young-Earth creationism to teach its introductory microbiology course this semester:

I can, at least in principle, imagine a creationist professor who taught the contents of a microbiology curriculum, complete with the common descent of life on Earth, and never breathed a word of his personal beliefs in the classroom. Could Gordon Wilson—of all people—be that “gold-star” creationist?

I decided the only way to answer that question was to ask Gordon Wilson.

Wilson, you may recall, appeared on D&T before, many moons ago. To find out what he had to say for himself, go read the whole thing.◼

Science online, one in twenty edition

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One in a billion Photo by Micah Sittig.

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Science online, caricatures of ant toiletry edition

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Crowd Is it getting crowded in here? Photo by James Cridland.
  • This week, at Nothing in Biology Makes Sense! The evolutionary compromise made by attractive flowers.
  • And, at The Molecular Ecologist: I mused about how science depends on what scientists notice.
  • Actually a pretty tidy solution. Ant larvae are completely constipated.
  • Woah. Has NASA captured images of water flowing on Mars?
  • Turning somersaults to remain inside the cave. The mental gymnastics of creationism.
  • Drosophila-philiac. A history of the fruit fly as a model organism.
  • Maybe not scary? No, that’s still a lot of people. Some fresh projections for world population growth—and a great in-depth report on the successful history of family planning in, of all places, Iran.
  • Where to even start? Fighting the good fight for science literacy online.
  • Hmm. Why don’t we have any numbers on the usefulness (or lack thereof) of online classes for minority students?
  • Because they’re designed to! When statistics make caricatures.
  • Superb. The endosymbiosis at the origin of eukaryotic life.
  • Step aside, Tyrannosaurus. Some fossil mammals that are just as cool as dinosaurs.

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The Molecular Ecologist: Noticing what we scientists notice

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"Regular" GFP A GFP-tagged nematode, and also a metaphor of sorts. Photo by Andy Peters.

Over at The Molecular Ecologist, I’m doing some musing about how scientific progress is shaped by what attracts the attention of scientists.

The probable selective impact of Joshua tree’s pollinators is obvious—it easily catches in the sieve of our attention and our desire to work with interesting critters. But I think it’s also fair to ask how much an interaction as specialized as the Joshua tree pollination mutualism actually tells us about the evolution of much more common, much less finely co-adapted relationships.

Do you ever worry that your study system limits what you can, well, study? Go read the whole thing, and tell us in the comments there.◼

Nothing in Biology Makes Sense: A flower is an evolutionary compromise

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Pollination IMG_4730D Welcome, pollinators! But, um, everyone else can just stay out, okay? Photo by Yeoh Thean Kheng.

Over at Nothing in Biology Makes Sense!, I’ve written about a neat study of the tropical vine Dalechampia scandens, which has to solve an evolutionary puzzle that confronts most flowering plants:

But there’s a downside to making a big, showy display to attract pollinators—you might also attract visitors who have less helpful intentions than gathering up some pollen and moving on to the next flower. Showy flowers might attract animals that steal the rewards offered to pollinators—or they might attract animals that eat the flowers themselves, or the developing seeds created by pollination.

To see how a team of biologists directly measured this evolutionary compromise (spoiler: it involves counting pollen grains with a hand lens) go read the whole thing.◼

Science online, yet another final argument edition

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First Stars There’s probably at least one class-M planet somewhere in this picture. Photo by redeye^.
  • This week at Nothing in Biology Makes Sense! Stalking the wild holobiont.
  • And at The Molecular Ecologist: How to “triangulate” your genome scan.
  • The fault is not in the stars, but in our telescopes. Will we ever find Earth-like planets orbiting other stars?
  • Wow. With winter precipitation at a record low, California is facing the third year of a catastrophic drought.
  • It is a truth universally acknowledged, that a scientist in possession of a hypothesis must be in want of Jane Austen. Jonathan Eisen takes issue with some literary advice for scientists.
  • A review of The Signal and the Noise. Why scientists need prior knowledge.
  • Yeah … probably not. Is this comparative karyotype the final piece of evidence that will shut down creationism?
  • In memoriam, Philip Seymour Hoffman. The science of addiction, in very personal perspective.
  • Wow. How a photographer caught a bee mid-sting.
  • The flaw in their thinking is the implicit assumption that a cat is a rigid body, an assumption that is obviously false to any cat-owner! The physics that lets cats land on their feet.

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The Molecular Ecologist: Triangulating the targets of natural selection

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torridon view Photo by paul.mcgreevy.

At The Molecular Ecologist, guest contributor K.E. Lotterhos discusses an important consideration in designing studies that “scan” the genome for regions experiencing natural selection—to be truly informative, they must “triangulate” using independent data:

Let’s say a number of individuals were collected from heterogeneous environments on the landscape. Some SNPs were significant both in an FST outlier analysis and a [genetic-environement association]. Would we consider these SNPs to have two independent sources of evidence?

NO, because the two tests were performed on the same sets of individuals.

What counts as “independent” in this context? I think that’s still something of an open question—but go read the whole thing and se what you think!◼