Category Archives: blogrolling

The Molecular Ecologist: Charles Goodnight

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Ants and Aphids, Backlit Photo by binux.

Over at The Molecular Ecologist, John Stanton Geddes continues his interview series with quantitative geneticist Charles Goodnight, whose work covers everything from multi-level perspectives on natural selection to the the causal linkage between directly measurable trait variation and interactions between individual genes. Here’s a sample of what Goodnight has to say about the group selection versus kin selection debate (which I’ve discussed here before):

Why the controversy continues today is not so clear. It is interesting that it is mostly very one sided. Those who champion group selection tend to understand kin selection, and dismiss it because it is not useful to them. Those who tend to champion kin selection tend to not understand group selection and dismiss it because it is a priori wrong.

The interview also covers Goodnight’s thoughts about how molecular genetics has changed the field since his days in graduate school, his experience starting up the blog Evolution in Structured Populations and his estimation of the probability of extraterrestrial invasion—I recommend reading the whole thing.◼

The Molecular Ecologist: Crowd-sourcing natural history

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Moths in an insect drawer Insects in a museum collection. Photo by Leeds Museum and Galleries.

This week at The Molecular Ecologist, I discuss some emerging initiatives to collect biodiversity data with a little help from the entire Internet:

… the websites iSpot and eBird ask volunteers to record their natural history observations directly, creating crowd-sourced records of species occurrences. (iSpot covers everything from amphibians to fungi, while eBird is specialized exactly as you would expect from the name.) Both of these sites provide educational resources in concert with their data-collection missions; iSpot through user-generated quizzes, eBird by helping bird-watchers find new species in their own neighborhoods. And both of them make their datasets public.

Have you ever worked with crowd-sourced data like this? Go read the whole thing, and tell us about your experience in the comments.◼

Nothing in Biology Makes Sense: Adjunctivitis

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2006.10.21 - Life Sciences South, University of Idaho The life sciences building at the University of Idaho. Photo by jby.

Over at Nothing in Biology Makes Sense! Noah Reid tackles the question that was left hanging in my recent article about a six-day creationist teaching introductory microbiology at the University of Idaho: how a person with such questionable credentials could have been hired in the first place. Noah argues that it’s a symptom of the poor treatment of adjunct faculty in American higher education.

These faculty are hired on a course by course, semester by semester basis. They receive no benefits and don’t have a shred of job security. By some estimates an average “full-time” adjunct faculty member teaching 8 courses a year (3 each semester and 2 in the summer, perhaps?) would make less than $30,000 a year and it’s thought that adjunct faculty are now doing 70% of the teaching at higher education institutions in the US.

… In response to this, I want to use a recent post at this blog to highlight a slightly less well covered aspect of the issue and the other side of that coin: when you offer shitty compensation, you might just get shitty employees.

To see the argument in full, go read the whole thing. Edited to add: and see also P.Z. Myers’s blistering reaction.◼

Queer in STEM: What’s the relationship between openness and comfort?

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Faculty members who are out to their colleagues are … much more likely to describe themselves as “uncomfortable”? Figure 1 from Patridge et al. (2014).

Over at the Queer in STEM site, I discuss the first study to try and tackle the questions that motivated QiS, which was just recently published. It’s exciting to see that other folks are also looking at the experiences of LGBTQ folks in STEM careers—but it’s a bit puzzling that this new study found a pattern very different from what we see in our own data:

… of the STEM faculty who answered the Campus Pride survey, those who who rated their “outness” level as 4 or 5 were much more likely to say they were uncomfortable in their department.

… In the most comparable analysis from our own study, we found that participants who described their workplaces as “welcoming,” or said they were “treated the same” as their straight colleges, were much more likely to be out to their colleagues—exactly the opposite of the relationship Patridge et al. found between begin out and feeling comfortable.

In the full post, I discuss some hypotheses about why we might have found such completely different results, and try to evaluate them based on the Queer in STEM data.◼

The Molecular Ecologist: Tracing soft selective sweeps in your gut microbiota

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ποντίκι / μυς, mouse (Mus musculus) by George Shuklin Why is my poop glowing blue? Photo by George Shuklin.

Over at The Molecular Ecologist, I’m discussing a new study that traces the adaptation of bacteria moving into a mammalian gut:

João Barroso-Batista and colleagues at the Instituto Gulbenkian de Ciência and Instituto de Tecnologia Química e Biológica in Portugal first treated mice with streptomycin to clear their guts of bacteria, then fed them cultures of Escherichia coli that were genetically uniform—except that half the E. coli cells in the culture had been engineered to produce a blue fluorescent protein, and half had been engineered to produce a yellow fluorescent protein. … If a single mutation made that one cell so successful that its descendants entirely dominated the gut, the authors would be able to tell—by checking the color of the host mouse’s poop.

To find out what the study’s authors learned by sequencing the bacterial genomes in that colored mouse poop, go read the whole thing.◼

Nothing in Biology Makes Sense: Dispersal versus mutation, on the edge

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Cane Toad at Daintree Village A cane toad, living in an evolutionary “Olympic village”? Photo by tubagooba.

This week at Nothing in Biology Makes Sense!, Devin Drown explains the population dynamics that crop up near the edge of a species’s geographic range:

One famous example of this phenomenon is found among invasive cane toads (Rinella marina) in Australia. In 2006, Phillips et al found that the toads at the leading edge of the expansion had longer legs making them primary candidates for high dispersal capabilities. Later, Lindstrom et al (2013) found (via radio collar measurements) that those toads at the front of the range were more likely to disperse than those at the encamped within the population.

To find out why biologists have compared life on the range edge to living in the athletes’ dormitory at the Olympics, go the whole thing.◼

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.◼

The Molecular Ecologist: Reviewing the causes of population genetic structure

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distance Photo by eliassss.

At The Molecular Ecologist today, I highlight a couple of recent literature reviews that seek to understand how natural populations are structured by the limitations of distance, and by local adaptation:

Taken together, these two papers are a nice compilation of a very large literature. If nothing else, they demonstrate that we’re well past the point of asking whether environmental isolation happens at all—in fact, it looks to be quite common—and we’re ready to start digging into the details of when and why it develops.

To see what broad patterns two different groups of authors were able to extract from their surveys of many population genetic studies, go read the whole thing.◼

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.◼

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.◼