Carnival roundup: Berry-go-Round and Diversity in Science


On the last day of April, two blog carnivals—collections of links to posts on a given topic—are freshy posted, and both are worth some of your surfing time.

First, over at Seeds Aside, is a double March/April edition of Berry-go-Round, which rounds up online writing about all things botanical, with everything from peppers to savannah treetops to electrical signalling within the tissues of carnivorous plants.

And then over at her blog on Scientopia, Scicurious is hosting an edition of the Diversity in Science Carnival devoted to “imposter syndrome,” the nagging fear of secret inferiority that almost everyone seems to feel at some point in a scientific career. Imposter syndrome can be especially troublesome for women and members of minority groups, who may not see many folks that look like them amongst their colleagues.

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 Noah: New surveys of a small nature reserve in Madagascar have turned up 36 previously unknown species of frogs.

Lead author of the paper, Gonçalo M. Rosa, told that the reason why this forest held so many frog species “is still a mystery.” He notes that up to 24 of the species in the forest may be endemic, i.e. found no-where else in the world but in tiny Betampona [Nature Reserve].

“And that’s why these numbers are so extraordinary (especially compared with other tropical forests),” Rosa exclaims. “Betampona is also considered a botanical ‘hotspot’ with 20 of the 100 most endangered Malagasy plants found within its borders!”

From Devin: Doctoral students could win a trip to Brussels from AAAS by turning their dissertation research into a dance.
The rules are simple. You must make a dance that not only captures the essence of your science but is also a cool work of art. Take a look at last year’s finalists for inspiration. Then enter the contest on the Gonzo Labs Web site. The competition is open to anyone in the sciences, broadly defined—engineers, mathematicians, and historians of science are welcome. You just need to be working on a Ph.D. or already have one. [links sic]
From Sarah: A new study finds that great tits (Parus major) are more likely to help other tits chase away predators if they know the other birds well.

“There are two explanations,” Ms Grabowska-Zhang told BBC Nature.

“One: birds join their neighbours because they think: ‘My nest could be next.’

“Or they join because their neighbours have joined their [predator chasing] mobs before, and they know that if they don’t reciprocate, they’ll be left alone next time. It’s sort of great tit tit-for-tat.”

From Jon: Women’s hearts may be more adversely affected by stress than men’s, based on measurements taken before and after a mental stress test.
This differing characteristic could potentially predispose women to heart problems while under stress, says study leader Chester Ray. He adds that the results came as a surprise, since previous studies men have significantly less blood flow than women during the physical stress of exercise, and could explain why women tend to have more heart troubles after stressful events, such as losing a spouse. The findings also reemphasize the importance of mental stress in affecting health.
Alongside the numerous cosmetic genital procedures he offers, Dr Ostrzenski trains practitioners in procedures including ‘g-spot fat augmentation’ and ‘g-spot surgical augmentation’. [link sic]

Genetic Auditing

For those of you who don’t dabble* in genetics, we’re in the midst of a major revolution. New technologies have literally transformed the questions we can ask and the data we can gather. It is currently possible (although not always advisable) to collect hundreds of gigabases (that’s 10^11) of data in a single run of a “high-throughput sequencer” (HTS). As a reference, I think there were 10^5 bases in my entire master’s thesis which, let me do the math, means one run on a HTS is equivalent to 1,000,000 of my theses?!?! Although that makes me a little queasy, it’s obvious and amazing progress.

Anyway – what can we do with these awesome new technologies? Coghlan et al. have found novel use, published in a recent PLoS Genetics.

"Bear Bile Crystals". One of the samples genetically audited for illegal and harmful components. From Figure 1 of Coghlan et al. (2012).

Traditional Chinese medicines (TCMs) have been used to remedy maladies for thousands of years. The popularity of TCM as a primary, secondary or supplementary medical practice has grown to the point where it is a multi-million dollar industry. TCMs rely heavily on plant and animal components – some of which can come from highly endangered (and thus illegally acquired) species or be harmful to the user. However, determining exactly what’s in a pill or powder isn’t as easy as reading the label.

HTS to the rescue!

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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 Jon: Many kids diagnosed with attention-deficit hyperactivity disorder may be having trouble sleeping, instead.

“No one is saying A.D.H.D. does not exist, but there’s a strong feeling now that we need to rule out sleep issues first,” said Dr. Merrill Wise, a pediatric neurologist and sleep medicine specialist at the Methodist Healthcare Sleep Disorders Center in Memphis.

The symptoms of sleep deprivation in children resemble those of A.D.H.D. While adults experience sleep deprivation as drowsiness and sluggishness, sleepless children often become wired, moody and obstinate; they may have trouble focusing, sitting still and getting along with peers. [Links sic.]

From Sarah: Fencing off a Hawaiian peninsula to keep out non-native predators—including cats, dogs, and, yes, mongooses—is letting native birds and other species recover.

“The fence is doing its job,” said Eric VanderWerf, a biologist who, with his wife, Lindsay C. Young, is studying populations of albatrosses and shearwaters on a grant from the Packard Foundation. “The cats and mongooses were killing 15 percent of the chicks every year, and now they’re all gone.”

Each week, Dr. VanderWerf drives from Honolulu to check a system of 1,100 traps, cameras and poisoned-bait stations for any indication that a predator may have sneaked in. [Link sic.]

From Devin: A new review of computer simulation methods in ecology suggests it’s better to pair complex simulations with simpler mathematical models.
The increasing use of computer simulation by theoretical ecologists started a move away from models formulated at the population level towards individual-based models. However, many of the models studied at the individual level are not analysed mathematically and remain defined in terms of a computer algorithm. This is not surprising, given that they are intrinsically stochastic and require tools and techniques for their study that may be unfamiliar to ecologists. Here, we argue that the construction of ecological models at the individual level and their subsequent analysis is, in many cases, straightforward and leads to important insights.
And from Jeremy: biochemists have synthesized new DNA-like molecules, based on different structural components, that can store and replicate genetic information.

[Vitor] Pinheiro created his XNAs by tweaking a natural enzyme called DNA polymerase, which copies DNA. It ‘reads’ a piece of DNA, grabs nearby bases, and assembles a matching strand. If you set the polymerase loose upon its own gene, you can get the enzyme to make more copies of itself.

Here’s the clever bit. DNA polymerase is normally very fussy about the bases it grabs. It only selects ones with a deoxyribose sugar so that it assembles DNA, rather than any other nucleic acid. But Pinheiro evolved the enzyme so that it prefers to use the building blocks of his XNAs instead.

Notes from the field: What’s Chris doing to that Joshua tree?

ResearchBlogging.orgMy postdoctoral research is shaping up more and more to be hardcore bioinformatics; apart from some time spent trying to get a dozen species of peanut plants to grow in the greenhouse as part of a somewhat long-shot project I’m working on with an undergraduate research associate, I mostly spend my workday staring at my laptop, writing code. It’s work I enjoy, but it doesn’t often give me an excuse to interact directly with the study organism, much less get outdoors. So, when Chris Smith dropped the hint that he could use an extra pair of hands for fieldwork in the Nevada desert this spring, I didn’t need a lot of persuasion.

Chris is continuing a program of research he started back when he was a postdoc at the University of Idaho, and which I contributed to as part of my doctoral dissertation work. The central question of that research is, can interactions between two species help to create new biological diversity? And the specific species we’ve been looking at all these years are Joshua trees and the moths that pollinate them.

Joshua trees, the spiky icon of the Mojave desert, are exclusively pollinated by yucca moths, which lay their eggs in Joshua tree flowers, and whose larvae eat developing Joshua tree seeds. It’s a very simple, interdependent interaction—the trees only reproduce with the assistance of the moths, and the moths can’t raise larvae without Joshua tree flowers. So it’s particularly interesting that there are two species of these highly specialized moths, and they are found on Joshua trees that look … different. Some Joshua trees are tall and tree-ish, and some Joshua trees are shorter and bushy. Maybe more importantly for the moths, their flowers look different, too.

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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 CJ: A list of 17 examples of humorous taxonomic names. No, but really.

Better known as the Conquered Lorikeet, Vini vidivici was a South Pacific parrot that went extinct roughly 700-1300 years ago. The name derives from the phrase “veni, vidi, vici,” which means “I came, I saw, I conquered.

From Sarah: The BBC explores the health effects of your internal microbial ecology.

What experts like Birren are discovering is the powerful role these tiny bugs might be playing in our lives. The 1,000-or-so species of microbes that live in our guts control digestion, and possibly so much more. They are strongly linked with the rise in allergies and asthma, and with digestive problems like Crohn’s disease and colitis. They also influence the immune system, and there is a growing body of evidence suggesting that gut microbes could have an influence on cancer risk. They could also dictate whether we are packing on extra pounds or liable to get diabetes. [Links sic.]

And from Jon: An article in the Journal of the American Medical Association introduces Choosing Wisely, an initiative devoted to avoiding unnecessary medical procedures.

The polarizing political environment makes it difficult to conduct rational public discussions about this issue, but clinicians and consumers can change the nature of this debate to the potential benefit of patients, the medical profession, and the nation. The initial focus should be on overuse of medical resources, which not only is a leading factor in the high level of spending on health care but also places patients at risk of harm. In fact, some estimates suggest that as much as 30% of all health care spending is wasted.

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 Noah: Ornithologists find that city-dwelling white-crowned sparrows change their songs to be better hear in the midst of urban noise.

“It shows a strong link between the change in song and the change in noise,” says David Luther, term assistant professor in Mason’s undergraduate biology program. “It’s also the first study that I know of to track the songs over time and the responses of birds to historical and current songs.”

From Sarah: New fossils reveal that an evolutionary ancestor of Tyrannosaurus Rex was the largest known animal to be covered in feathers.

With a Latin and Mandarin name translating to “beautiful feathered tyrant,” Yutyrannus huali was found in the Yixian Formation, a fossil deposit in northeastern China that over the last two decades has yielded dozens of dinosaur skeletons so finely preserved that it’s possible to discern feather-like structures.

Those discoveries have fundamentally changed how dinosaurs appear in our imagination’s eye. Contrary to traditional artistic interpretation, many — perhaps most — of the great reptiles were not covered in scales, but rather with feathers. [Link sic.]

From CJ: Hybridization between two species of blacktip shark may be helping one of the species adapt to climate change. (But what’s up with that headline?)

Australian blacktips confine themselves to tropical waters, which end around Brisbane, while the hybrid sharks swam more than 1,000 miles south to cooler areas around Sydney. Simpfendorfer, who directs the university’s Centre of Sustainable Tropical Fisheries and Aquaculture, said this may suggest the hybrid species has an evolutionary advantage as the climate changes.

From Jeremy: To overcome imposter syndrome—the nagging worry that you’re not as smart or skillful as your peers—maybe science should try to be more like sports.

Sure, I have as many bad days training and racing as I do in the lab, and I’m probably competing against WAY more people, but then, failure in running just doesn’t seem to hurt as much, there’s always the feeling in running that you can pick yourself up, work a little harder, come back a little stronger, and try again. Of course, there’s the fact that this isn’t my career, but still, even so, a bad race just doesn’t mess with my head. It rolls right off, I feel bad for a day, and then I get back up driven to do better at my next one.

Help us make sense!

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Are you a working biologist, biology student, or other person with a first-hand connection to the living world? Do you like reading science blogs—including maybe this one—and wonder what it’d be like to get into this online-popular-science-writing thing? Or do you have your own science blog already, and want to expand your audience? Then you should consider writing a guest post for Nothing in Biology Makes Sense!

We’ll prioritize contributions from folks who work in biology in a broad sense—anything from medicine to basic research, at career stages from students to professors. And, true to our headline, we’ll be especially interested in pieces that show how something in biology makes sense, if you think about it in light of evolution.

Wondering what a good guest post looks like? Check out previous ones by Tom Houslay, Colin Beale, and James Winters.

So what are you waiting for? E-mail Jeremy to propose a post and discuss scheduling.

Multidimensional coevolution, no oscillation overthruster required

Gilman etal 2012 wordleConventional wisdom suggests that pathogens and parasites are more rapidly evolving because of various reasons such as short generation time or stronger selection. Yet somehow, they have not completely won the battle against the host. Recently, a theoretical paper on coevolution in Nature caught my eye (Gilman et al., 2012). Here the authors address this paradox: “How do victim species survive and even thrive in the face of a continuous onslaught of more rapidly evolving enemies?

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.

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Introducing the Black Queen Hypothesis

A paper by Morris and colleagues (2012) has generated some stir among biologists. The authors are proposing the Black Queen hypothesis to explain genomic reductions among free living interacting microbes. Rather than rehash arguments that have been made more eloquently, I’d like to just point out some informative ones

Quick summary over at the New Scientist

In depth critique by Robert T. Gonzalez

Tommy Leung also reminded me of a great review paper by Sachs et al (2011) over at TREE that is highly relevant to this debate.