Friday Coffee Break


Here’s what we’ll be talking about while we wait in line for a latte:

How to get ants to carry a sign for you. From Jeremy.

Amazonian builder of mysterious tiny picket fences sort of discovered. From Amy.

Scientific meetings feature more women speakers when women are included in the organizing committees. From Sarah.

PLOS ONE papers that made the news in 2013. From Sarah.

A personal account of growing up unvaccinated in the 1970s. From Jeremy.

Even tiny roads built through amazon rainforest disrupt canopy-dwelling frog communities. From Noah.

On the evolution of blind cave fish.

Astyanax mexicanus cave dwelling form.

Evolution requires variation in traits among individuals to act. If evolutionary fitness is determined by a given trait, and everyone in a population has the trait, then there is no basis for natural selection to discriminate among individuals. Furthermore, when variation does exist, it must be genetically based so that it can be passed down by successful parents to their offspring. The trait variation on which selection acts can either come from genetic variation existing in a population before selection begins or it can result from new mutations. Because natural selection acts to eliminate unfavorable variation, there is a question as to how selection in a changing environment could reverse change, or remove a trait it had previously favored. Where would the necessary variation come from?

One controversial hypothesis is that genetic variation for a given trait can be masked from selection by very stable (or “canalized”) developmental processes. These canalized processes result in highly uniform traits within a population despite underlying genetic variation. Under certain environmental conditions (in particular, stressful ones), they can be destabilized, allowing underlying genetic variation to cause traits to vary, thus providing grist for natural selection’s mill.

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Friday Coffee Break! Jules-likes-the-links Edition.


Here’s what we’ll be talking about while we wait in line for a latte:

Are you unreasonably paranoid about germs? New proposals by the FDA  may add a lot of stress to your life. The rest of us, however, should be quite happy about them.

A discussion of the ecological “ghosts” of extinct birds in the ecosystems they inhabited.

A pair of videos about urgent environmental issues utilizing very effective visuals, one on road building and deforestation and a second on overfishing.

A NEW TAPIR species has been discovered. When a 100kg mammal flies under science’s radar for so long (local indigenous people knew it was different all along…) you know we have a terrible grasp of earth’s biodiversity.

This week in genetics/popular science controversies: DNA sequence motifs that regulate gene expression are found to overlap with sequences coding for proteins far more frequently than previously thought. This may explain some prominent and heretofore mysterious features of protein coding DNA. An unfortunate attempt at coining a new term (“duon”) and blundering PR campaign about the work inspire some stinging rebukes.

Friday Coffee Break: You talkin’ to me? You talkin’ to me!?


Here’s what we’ll be talking about while we wait in line for a latte:

War. War never changes. Argentinian mockingbirds brutally attack brood parasitic cowbirds, but fail to stop them from laying eggs. -From Noah.


But Wait! There’s More! The jet-propulsion butt-hydraulic system also is a gill.” -From Jeremy, who tells me that Apple and Samsung are currently waging a high-stakes patent battle over the butt-hydraulics to be included in the next generation of smart phones. 

Finally, in keeping with the belligerent theme: David Dobbs writes an adversarial piece on the concept of the selfish gene and Richard Dawkins and Jerry Coyne rebuff it. Meanwhile, Michael Behe [link redacted] says something that makes everyone ask “Must creationist effluvia befoul every. single. google search I do for this blog?”

Friday Coffee Break: Just what is a Denisovan Anyway?

They’ll never believe you.

Here’s what we’ll be talking about while we wait in line for a latte.

From Sarah: Drug cartels and academia share similarly structured labor markets.

…and in that cynical vein, a statistical analysis using professors’ last names that shows nepotism is a significant force in Italian universities.

From Noah: A new record is set in ancient human DNA sequencing: 400 thousand year old hominid DNA has been successfully sequenced. The results suggest previously unknown complexity in human history, and that we don’t really know what, exactly, the Denisovans were. Or at least they suggest that Noah doesn’t know.

It’s an old reference, but it holds up: check out this ten year old David Foster Wallace essay, “Consider the Lobster“. For an article in a food magazine, it sure has a lot of interesting lobster biology in it.

We may be late to the party on this one, but there has been some interesting debate about the role the FDA should have in human genetic testing, particularly as it relates to the company 23andme’s direct-to-consumer model. Here is Michael Eisen’s take. Also, a blog post on the statistical issues associated with large scale screening for disease-associated genotypes has generated some interesting discussion (23andme genotypes are all wrong).

Meanwhile, 23andme has decided to stop offering health-related interpretation of the genotype data they provide.

Learn the origins of fairytales with this 1 weird trick!

Figure 4 from Tehrani 2013. The result of a network analysis among fairy tales. The large number of well spaced network connections from the East Asian group is suggestive of blending between the other two major groups.

Figure 4 from Tehrani 2013. The result of a network analysis among fairy tales. The large number of well spaced network connections from the East Asian group is suggestive of blending between the other two major groups.

In a pretty interesting example of cross fertilization between scientific disciplines, a recently published paper by Jashmid Tehrani uses phylogenetic methods borrowed from evolutionary biology to construct an “evolutionary tree” of fables related to Little Red Riding Hood.

Tales typical of Riding Hood are found mostly in Europe, but a series of stories sharing some features are found in Africa (involving an Ogre) and East Asia (The Tiger Grandmother). These have sometimes been considered to be part of the Riding Hood group, but there has been debate over whether or not they actually belong to another, closely related group found in Europe and the Middle East known as The Wolf and the Kids.

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52 million year old fossil sheds light on swift and hummingbird flight evolution

IMG_4718  Whiskered Tree Swift (female)

This week we have a guest post by Jessica Oswald a graduate student at the Florida Museum of Natural History at the University of Florida. She works on the biogeography of neotropical birds using fossil, ecological, and molecular genetic data.

As an avian paleontologist, digging through fossils is to me like birding with a time machine. These fossils help us paint a picture of where modern forms came from and how different ancient species were from modern-day birds, especially intermediate forms. These outliers and in-betweeners are interesting because they hint at all sorts of morphological diversity that we don’t even know or expect, and give us a window into the past and how different diversity, communities, and climatic conditions and landscapes were from what we are familiar with today.

This paper (Ksepka et al. 2013) on an early bird in the Swift-hummingbird clade does both of these things by exhibiting an odd morphology that we don’t see in modern birds, and helps us understand how the uniquely specialized wing shapes in modern swifts and hummingbirds arose from their common ancestor.

Members of the order Apodiformes: treeswifts (Hemiprocnidae), true swifts (Apodidae), and hummingbirds (Trochilidae), are aerial marvels. Swifts are able to reach the highest speeds during level flight (Chantler 1999) and hummingbirds are well known for their hovering abilities and their sideways and backward flight. Swifts and hummingbirds, while sharing the same wing bone characteristics, have different lengths of flight feathers, resulting in different wing shapes across the group, which allows them to perform their different aerial feats. Hummingbirds have shorter wings relative to their body size compared to swifts, resulting in their hovering abilities. These different wing shapes are well suited for their modern functions, but we have almost no fossils from this group, so we don’t know how the wing shapes diverged, or anything about the ecology of ancient species in this lineage.

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Better know your bacon: the evolutionary history of the genus Sus.

Wild Boar In Snow

It would seem that between the global hitchhiking of feral pigs with human migration, America’s absurd obsession with bacon and the possible emergence of pandemic influenza via recombination of human and porcine strains, the past, present and future of our civilization are inextricably linked to that of the domestic pig. With that in mind, let’s have a look at a recent paper on the evolutionary history of the genus Sus by Frantz et al. 2013.

Domestic pigs are in the family Suidae, which includes the babirusas, warthogs, the endangered pygmy hog (whose generic name is, Porcula, seems a likely candidate for America’s next tragic children’s cereal) and the domestic pig’s close relatives in the genus Sus. Depending on where you draw the lines, there are around 7 species in Sus. With the exception of the wild boar (Sus scrofa) their natural ranges are restricted to Southeast Asia west of Wallace’s Line. Extant species of Sus have diversified recently (sharing a common ancestor ~5 million years ago) and the species are all thought capable of producing viable hybrid offspring. Most species are restricted to single islands or island complexes in Southeast Asia (such as Borneo, Java and the Philippines). Previous phylogenetic estimates of the genus are in conflict over the relationships among species.

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Missed Connections: reproductive isolation and diversification rate

MissedConnections“You: on the earth’s surface. so young. so dynamic. full of life and suggesting a world of possibility. Me: subterranean. really old. fossilized, almost. intriguing but slightly inscrutable. We brushed past each other in Rabosky and Matute (2013). I thought there was something there, but in the blink of a p-value you were gone.” 

One of the perennial questions in evolutionary biology is “What factors determine how many species are on earth?” Researchers take numerous approaches to get at this very big question. One is to look for correlations between attributes of organisms, the environments they inhabit, or geologic history and rates of species diversification. This the study of macroevolution, and it is based on the idea that the discovery of these correlations on large scales (often using datasets with hundreds to thousands of species with deep histories spanning tens of millions of years) would be a powerful indicator of the factors governing species richness. Another approach is to study speciation on a small scale, to examine sets of closely related populations currently in the process of diverging. The thought is that if we can observe the forces driving divergence in contemporary populations, we can use those observations to develop a more general understanding.

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Of Salty Bahamian Ponds and Adaptive Radiation

A Mexican pupfish, Cyprinodon veronicae

One of the central hypotheses about how the diversity of life is generated is known as “adaptive radiation“. This term, popularized by G.G. Simpson in the mid 20th century, encapsulates an idea that is relatively easy to grasp: that the spectacular arrays of morphological and species diversity that we observe in the world are often the result of great bursts of speciation and morphological change. These bursts occur because a single species colonizes a new area, acquires a new adaptation, or suddenly escapes its competitors or natural enemies (possibly by their extinction). This opens up a new universe of possible lifestyles that evolution then drives that species to take up by rapid diversification. Think of the Hawaiian honeycreepers or Darwin’s finches.

The idea holds great sway because it is simple and powerful, but testing it empirically has proven very difficult. This is in part because the actual mechanisms underlying speciation and morphological diversification are exceedingly complex, and in part because many of the groups of organisms which we suspect have adaptively radiated did so long ago, leaving much of the evidence of those mechanisms buried under millions of years of subsequent evolutionary change. A recent experiment by Martin and Wainwright (2013) attacks these issues by manipulating a nascent adaptive radiation of Cyprinodon pupfishes on the island of San Salvador, Bahamas.

Cyprinodon are small fishes that have a habit of becoming isolated in unexpected places. In the United States they are best known for tentatively clinging to life in tiny springs in deserts of the southwest, where they’ve been embroiled in conflicts between conservation and urban and industrial interests over water rights. Almost all of them are dietary generalists that tend to eat a lot of algae. Martin and Wainwright’s study focused on three species that occur in another such unexpectedly isolated locale, a pair of hypersaline lakes on the island of San Salvador, Bahamas.

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