Category Archives: Nothing in Biology Makes Sense

Nothing in Biology Makes Sense: Searching for Ronald Fisher

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Geneticist Ronald A. Fisher. Photo via WikiMedia Commons.

This week at the collaborative science blog Nothing in Biology Makes Sense!, my lab-mate John Stanton-Geddes writes about the current state of evolutionary genetics, as presented at the recent Evolution meetings in Ottawa:

One theme that emerged through the meeting was “The genetic basis for [insert trait here]. While this goal of mapping phenotype to genotype has been a primary goal of many evolutionary ecologists since the first QTL mapping studies, it has recently come under strong criticism, notably in a fantastic paper by Matthew Rockman in the journal Evolution last year, but also by Pritchard and Di Rienzo 2010 and in a forthcoming article by Ruth Shaw (full disclosure: Ruth was my PhD advisor) and Mike Travisano.

Readers of Denim and Tweed will recognize that John’s complaint about our ongoing fixation (ha!) on individual genes of large effect mirrors some of my own recent thinking. So naturally, I think you should go read the whole thing.◼

Nothing in Biology Makes Sense: Merch that makes sense!

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Merchandising! Images from Denim and Tees.

If you enjoy the group science blog Nothing in Biology Makes Sense!—and I hope many of my readers here are also fans of NiB—you can now wear that appreciation on your sleeve. Or on your chest, anyway. NiB is officially launching its first merchandise, including tee shirts and coffee mugs bearing a selection of icons from the website header, and (with apologies to Theodosius Dobzhansky) a variation of the site’s slogan. All proceeds will go toward the costs of maintaining the site, so if you like the work we’ve been doing over there, go place an order.◼

Nothing in Biology Makes Sense: The changing landscape of ecology and evolutionary biology

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Scarlet monkeyflower, Mimulus cardinalis, is one of the new “field model organisms” developed for research thanks to advances in DNA sequencing technology—and a whole lot of work. Photo by Al_HikesAZ.

This week at the collaborative science blog Nothing in Biology Makes Sense!, guest contributor David Hembry, who’s just completed his Ph.D. in ecology and evolutionary biology, reflects on how much has changed since he started his doctoral research—in terms of methods, study organisms, and who his key collaborators are.

Some of the transformations in the field I think I could see coming. For instance, it was clear in 2005 that computational power would keep increasing, phylogenetics would be used more and more to ask interesting questions, more and more genomes would be available for analysis, and evolutionary developmental biology was on the rise. It was unfortunately also predictable that it would be possible to study climate change in real time over PhD-length timescales. And although the 2008 global financial crisis didn’t help, it was clear that funding and jobs were going to be more competitive than they had been for our predecessors.

But there were a number of things I didn’t see coming, and which have made the field look radically different than it was back in 2005.

For a detailed look at the last seven years of advances and shifts in the ways we study descent with modification, go read the whole thing.◼

Nothing in Biology Makes Sense: Making sense of genome reduction

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Over at the collaborative science blog Nothing in Biology Makes Sense!, guest contributor Levi Morran examines the processes by which bacteria can lose genes over generations of evolution.

In a recent paper, Lee and Marx (2012) test both how and why they observe large-scale patterns of gene loss in their experimentally evolved populations of Methylobacterium extorquens. They evolved these bacterial populations under different treatments of resource availability (realms of specialization) and found that all replicate populations adapted to their specific treatment over 1,500 generations. During experimental evolution, 80% of the bacterial populations exhibited nearly a 10% reduction in genome size, and many of the gene losses occurred in similar regions of the genome, some even across treatments.

To learn how and why those genes disappeared, go read the whole thing.◼

Nothing in Biology Makes Sense: Making sense of evolving invaders

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This week at the collaborative science blog Nothing in Biology Makes Sense, guest contributor Kathryn Turner discusses how evolutionary processes determine whether an introduced species becomes an invasive species.

First, most obviously, how is it that a species is able to come into a new environment that it is not adapted to, surrounded by new environmental conditions and foreign biological interactions, and thrive? Thrive so exaggeratedly, that it can out-compete and displace species which have been there for millennia, adapting precisely to those environmental conditions and biological interactions? How can an individual survive to propagate a population? How can any species accomplish this? Second, less obviously: why can’t more species do it? Humans transport animals and seeds (and spores and larvae, etc, etc) around all the time, but only 10% establish self-sustaining populations, and only 1% spread to new habitats, becoming potentially invasive; this is known as the ‘tens rule’ (Williamson 1993) – a funny ‘rule of thumb’ for which I could never quite figure out the math.

For the answers, or at least some ideas about possible answers, go read the whole thing.◼

Nothing in Biology Makes Sense: Making sense of polar bears’ origins

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Polar bear. Photo by ucumari.

This week at the collaborative blog Nothing in Biology Makes Sense, contributor Noah Reid goes in-depth on the recent study pinpointing the historical origins of polar bears, and why it’s taken the most recent systematic methods to correctly pinpoint them.

From 2008 to 2010, a series of algorithms were published that could take data from multiple genes and infer the history of whole populations, a drastic improvement over previous methods that could only identify the history of single genes (e.g. mtDNA). With these methods in mind, a group of researchers gathered data from 14 nuclear genes for multiple extant brown and polar bear populations (Hailer 2012). … the new data analyzed with the new method suggested that polar bears diverged far earlier than previously thought (around 600 thousand years ago) and that they were no longer closely related to the southeast Alaska population, but rather to the common ancestor of all brown bear populations.

For more details, including a nice brief explanation of why it can be important to use multiple genes in reconstructing relationships among species, go read the whole thing.◼

Nothing in Biology Makes Sense: The link between science and religious (un)belief

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The Thinker. Photo by marttj.

This week at the collaborative science blog Nothing in Biology Makes Sense, guest contributor Amy Dapper takes on a recent psychological study showing that people prompted to think analytically were subsequently reported less likely to report religious belief.

Their first study establishes a correlational relationship between analytic thinking and religious belief by asking participants to answer three clever questions that have an immediate intuitive, but incorrect, answer and a correct answer that requires deeper analytical processing. These questions, and their answers, can be found in the table below. The study participants then answered a survey about their religious beliefs. The results show that participants that arrive at the correct, analytical answers to the first set of questions also tend to exhibit more religious disbelief in their responses to the survey.

The results would seem to confirm the experiences of many of us working in science: when you think analytically Monday through Friday, it can be difficult to stop thinking that way on Sunday morning. For more detail on the experiments, go read the whole thing.◼

Nothing in Biology Makes Sense: What’s in my traditional medecine?

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Saiga antelope. Photo via Nothing in Biology Makes Sense.

This week at the collaborative blog Nothing in Biology Makes Sense, Sarah Hird explains how to identify the ingredients in traditional Chinese medecines—with a whole pile of sequence data.

[Coghlan et al.] target one animal and one plant marker and “genetically audit” the samples by sequencing the heck out of them using a bench-top HTS, the Roche GS Junior. Their protocol produced 49,000 sequence fragments. They then compare their sequences to large databases containing sequences of known origin and thus, identify what’s in the TCM.

To learn what the group found, go read the whole thing.◼

Nothing in Biology Makes Sense: You are coevolving in another dimension …

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Photo by Thomas Hawk.

This week at Nothing in Biology Makes Sense!, Devin Drown walks us through a cool new theoretical model that shows how hosts and prey species can evade parasites and predators in an ongoing coevolutionary struggle—if they each coevolve in multiple dimensions.

Instead of treating a coevolutionary interaction between two species as the interaction of only two traits, the authors investigate the nature of an interaction among a suite of traits in each species. It’s not hard to think of a host having a fortress of defenses against attack from a parasite with an arsenal loaded with many weapons.

Full disclosure: Scott Nuismer, one of the coauthors on the new model, has collaborated with me and with Devin. For more detail, go read the whole thing. ◼

Nothing in Biology Makes Sense: Making sense of “stinkbird” gut microbes

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A hoatzin. Photo by Carine06.

I was off the grid last week, so I missed Sarah Hird’s latest post at the group blog Nothing in Biology Makes Sense!, discussing a cool new study of the microbes in the guts of hoatzins, a species of wonderfully weird birds.

The hoatzin has an enlarged crop for the purpose of fermentation (see figure below). A “crop” is an anatomical structure in throat of some animals (including most birds) that primarily stores food. In the hoatzin, however, it does much, much more. Foregut fermentation is a digestive strategy where microbes living in or before the stomach break down vegetation for their host. Microbes are required by foregut fermenters because only the microbes are capable of breaking down the cell wall of plants, a barrier that confines most of the nutrients found in plant cells. The hoatzin is the only bird to use foregut fermentation and is the smallest known foregut fermenter.

To learn what the new study reveals about the diversity of microbes in hoatzin foreguts, go read the whole thing, including the evolving plans for follow-up experiments in the comments. ◼