Friday Coffee Break

coffee ( again)
Every Friday at Nothing in Biology Makes Sense! our contributors pass around links to new scientific results, or science-y news, or videos of adorable wildlife, that they’re most likely to bring up while waiting in line for a latte.

From Noah: A chain of events: Human hunting –> extirpation of large megafauna –> Australia’s wet rainforests become dry savannah.
Exploring sediment cores for past evidence of big herbivores, researchers found that the arrival of humans coincided with the loss of a menagerie of magnificent beasts, from giant kangaroos to fearsome marsupial lions and monster birds to Komodo dragon-like reptiles. The decline of this megafauna ultimately led to ecological changes that may have caused Australia’s rainforest to become savannah.
From Devin: A new independent overview of Peerage of Science appears in Trends in Ecology and Evolution:
PoS has the ambitious aim to enhance peer-review quality, save time for authors, reviewers and editors, and money for publishers. It is designed to be an open community, but reviews can only be written by scientists who have already published a peer-reviewed scientific paper. Manuscripts are submitted through the PoS web application, which allows peers to sign up for reviewing and subsequently automatically coordinates a four-stage peer-review process.
Also from Devin:  A short video describing a plant-bird mutualism from TEDEducation.

And from Sarah: A National Trust in the UK finds: Nature is good for you!
The trust argues, as have other bodies in previous years, that the growing dissociation of children from the natural world and internment in the “cotton wool culture” of indoor parental guidance impairs their capacity to learn through experience.

The Amazing Stinkbird

The hoatzin is an amazing bird. Look at it:

It’s awesome. The hoatzin is the only bird in the family Opisthocomidae and its taxonomic position amongst other birds is unresolved. It’s a weak flier and it smells bad (think cow manure) and both of these traits are due to the awesomest thing about the hoatzin: it’s a foregut fermenter.

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. It’s a weak flier because of the anatomical accommodations the enlarged crop requires. And it stinks because fermentation is an odoriferous process. (The bright side to being the Stinkbird is that the hoatzin is not eaten by humans and this probably contributes to the fact it is NOT endangered!)

Figure 1 from Godoy-Vitorino (2008); "Bacterial community in the crop of the Hoatzin, a Neotropical folivorous flying bird"

Figure 1 from Godoy-Vitorino (2008); "Bacterial community in the crop of the Hoatzin, a Neotropical folivorous flying bird"

And this brings us to today’s paper. Previous work from the Dominguez-Bello research group has characterized the crop microbiota (and by that I mean, sequenced the DNA of and taxonomically identified the bacterial species present). The goal of the current study was to compare the microbiota at a population level. Godoy-Vitorino et al. (2012) sampled three birds at two populations in Venezuela roughly 500km apart (6 birds total). At each site, they performed vegetation surveys (to identify potential food sources) and recorded about 30 hours of hoatzin foraging behavior. To compare the microbial communities, Godoy-Vitorino et al. used a PhyloChip – a microarray specifically for identifying bacterial species in a complex sample.

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Friday coffee break

Every Friday at Nothing in Biology Makes Sense! our contributors pass around links to new scientific results, or science-y news, or videos of adorable wildlife, that they’re most likely to bring up while waiting in line for a latte.

From Sarah: Going on a century after the Scopes trial, the Tennessee state senate has passed a bill that would permit teaching Creationism as science in public schools.

The sponsors say that it’s meant to improve science education and do all sorts of wonderful things. I think they’d say that it cleans your floors too, if you asked them. The effect of the bill, regardless of what they might want to say that it does, would be to make it harder for parents and teachers and administrators to make sure that science was being taught accurately in science classes. It would open the door to creationism, it would open the door to climate change denial, and to other sorts of pseudosciences being introduced into Tennessee classrooms.

And from Jeremy: A series of thought experiments illuminate the reasons why in statistics, numbers may not add up the way you think they should.

Now, on to statisticians, who take another view entirely. To them it matters what else could have been said and the interpretations that can pop up when math is released into the real world. “For example,” says Devlin, “we’re taught that multiplication is commutative, that 3 × 4 is the same as 4 × 3; but in the real world three bags of four apples isn’t the same as four bags of three apples.”

Crossing those curious parallels: language and biological evolution

The language of evolution (Darwin, 1859)

This post is a guest contribution by James Winters, the proprietor of  Replicated Typo, a group blog about language and evolution. James holds a MSc in the evolution of language and cognition from the University of Edinburgh, and is contemplating going on for a doctorate. If you have an idea for a post, and you’d like to contribute to Nothing in Biology Makes Sensee-mail Jeremy to inquire.

Just over 140 years ago, Charles Darwin famously discussed the striking parallels between the forces that govern language change and the evolutionary processes underlying species formation:

“The formation of different languages and of distinct species, and the proofs that both have been developed through a gradual process, are curiously parallel… We find in distinct languages striking homologies due to community of descent, and analogies due to a similar process of formation… We see variability in every tongue, and new words are continually cropping up; but as there is a limit to the powers of memory, single words, like whole languages, gradually become extinct” (Darwin, 1871: 78-79).

Darwin recognised, along with several other linguists of the period such as August Schleicher and Mikołaj Kruszewski, that language falls under the remit of evolutionary principles. Since then, there has been a renewed and growing interest in evolutionary (Croft, 2000) and ecological (Mufwene, 2000) theories of language change, with biological, cultural and linguistic forms of evolution being captured by the more general rubric of Complex Adaptive Systems. First coined by Holland (1992), CAS are a subset of nonlinear dynamical systems in that they exhibit emergent properties as a result of multiple, interconnected elements. However, it is the capacity to evolve and adapt that differentiates language and biology from these other systems, with the key concept being their ability to learn: past experiences filter through, or influence, future states of the system due to cumulative amplification dynamic (Deacon, 2010).

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Friday coffee break

Experimental coffee

NiB does not endorse drinking coffee at your lab bench. No, sir.

Every Friday at Nothing in Biology Makes Sense! our contributors pass around links to new scientific results, or science-y news, or videos of adorable wildlife, that they’re most likely to bring up while waiting in line for a latte.

From CJ: A new kind of DNA is found in short, circular snippets.

Professor Anindya Dutta and colleagues pruified DNA taken from samples of  tissue and then digested away the linear DNA (which consists of millions of base pairs) to leave only circular DNA pieces, which they then sequenced using ultra-high-throughput sequencing. Circles were identified by a new bioinformatics program. [Link sic.]

From Sarah: Parasitic wasps help two species of weevil to coexist.

Without the ever-present effects of a predator [the wasp], one of the two weevil species would die off within 20 weeks, the researchers found. If they introduced the predator wasp into the lab ecosystem, all three would survive for 118 weeks (the length of the study — that’s two years, three months and two weeks).

And, from Jeremy: A behavioral biologist explains her study of ground squirrels’ methods for scaring off rattlesnakes—using a robot squirrel.

Hands of Blue

Today’s post is going to be a little different from the standard of this site.  No, I’m not writing about Firefly, but I’ll get to that connection in a bit.  I would like to take the opportunity to give the readers of Nothing in Biology Makes Sense a brief glance into an aspect of medicine that few get the opportunity to experience.

I am talking about surgery, specifically, Cardiothoracic surgery, or surgery that takes place by opening up the chest of a patient and putting them on cardiopulmonary bypass in order to operate on the heart (doing coronary bypass, valve replacement, or placement of assist devices).  The reason I feel the need to post about this is because I know I have been given the opportunity that few people (physicians and medical students included) get the chance to experience first hand.  For the last 6 weeks I have been on my surgical rotation, and was lucky enough to be able to spend two of those weeks working with the Cardiothoracic surgeons observing and assisting with open heart surgeries.

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Friday coffee break


Every Friday at Nothing in Biology Makes Sense! our contributors pass around links to new scientific results, or science-y news, or videos of adorable wildlife, that they’re most likely to bring up while waiting in line for a latte.

From Sarah: Sequencing the genome of a 5,300-year-old body preserved in the ice of the Italian alps has revealed some interesting personal details.

The lactose intolerance makes sense, said Albert Zink, an anthropologist at the European Academy of Research in Bolzano, Italy, who was one of the study’s authors.

“In early times, there was no need to digest milk as an adult because there were no domesticated animals,” Dr. Zink said. “This genetic change took hundreds of years to occur.” [Link sic.]

And from Jeremy: An uprecedented study of genetic variation among the cells comprising individual tumors suggests that cancer genetics are going to get a lot more complicated before we understand them better.

Swanton found that even the primary tumour was surprisingly varied. He found 128 mutations among the various samples, but only a third of these were common to all of them. A quarter of the mutations were “private” ones – unique to a single sample.

The tumour had also split down two evolutionary lines. One area – part of R4 in the picture – had doubled its usual tally of chromosomes and seeded all the secondary tumours in the patient’s chest. The other branch had spawned the rest of the primary tumour. Even though this tumour looks like a single mass, whose cells all descended from a common ancestor, its different parts arehave all  evolved independently of one another.