From Amy: Analysis of DNA from museum specimens has identified the pathogen responsible for the Irish Potato Famine of 1845.

…the strain that changed history is different from modern day epidemics, and is probably now extinct.

From Sarah: Digital visualizations may be making it easier to teach students how to understand evolutionary trees. As in, for instance, this visualization of the phylogeny of birds.

Taxa appear as dots whose relative spatial distances are determined by phylogenetic relatedness. When reading a cladogram, the intuitive impulse to infer relatedness from spatial distance between branch tips inevitably leads to error. The DEM works with this intuition, rather than against it.

From Jeremy: Hard as it may be to believe, this FAQ about dealing with the bites of venemous snakes just keeps getting better as you go down.

Fungi are pretty. And the ones in your home are (hopefully) smaller than this.

I’m very excited to be going to this meeting in June that focuses on the microbiome (i.e., all the living microbes) of our built environment – our homes, work places, sewers, etc. I’m used to thinking about the genetics of much larger living things – like chipmunks – where large non-living things – like rivers – create barriers between populations within a species which allows the populations to evolve independently. It’s been surprisingly difficult for me to apply my background “macro” knowledge to my new “micro” interests. How do different microbial species arise? What is a microbial species, anyway? Specifically restricting my many questions to our homes – what barriers could cause divergence between seemingly connected individuals?

Bacteria abound on our skin and when we come in contact with items in our home, our bacteria are directly transmitted to the surface (think door knobs). Additionally, we shed skin cells – and their bacteria – in our homes resulting in a near constant snow of human-associated (and pet!) bacteria. These facts lead to human occupancy being a source of our indoor microbiome. But bacteria are not the only miniscule things sharing our living spaces. What about other microbes? And now for the question of the day: where does the fungi in your house comes from?

Adams et al. (2013) investigate this question in an ecological framework and they’re specifically interested in whether inhabitants or just the outside environment affect air-borne fungi. They focus on 11 apartments from a single housing complex to control as much as possible for effects of the environment. They collected airborne dust on sterile petri dishes suspended from the ceiling in one bedroom, one bathroom, kitchen and living room and outside on the patio. They collected once in the winter and once in the summer, interviewed residents regarding possibly important influences and monitored temperature and humidity at each location. (Note: these are air-borne fungi – this method does not allow them to talk directly about the fungi that have colonized surfaces.)

RESULTS! To gloss over a lot of cool details – Adams et al. found basically no evidence that we, the inhabitants, affect airborne fungi. They also found no evidence that similar rooms across apartments bear similar fungal communities (basically, bathroom fungi from one person’s house is not the same as bathroom fungi from another person’s house). So what DOES affect fungi?

1. Season. Both indoor and outdoor fungal communities show clustering by whether they were from the summer or winter (Figure 1). Winter samples contained more types of fungi and the authors note this is probably due to a climate that results in more winter sporulation.

Figure 1: The relationship between summer (orange) and winter (green) fungal community samples. (Supplemental Figure 4 from Adams et al. 2013)

2. Randomness. Indoor fungal communities were random subsets of the outdoor fungal communities and each apartment was basically distinct.

3. Distance. Units that were closer together had more similar fungal communities. This pattern of “isolation-by-distance” is a well-known and beloved observation/process in macro-biology and has been shown in microbes at large distances, but this study shows it on a very small scale (<500m). The authors conclude that this observed pattern is because fungi are limited in their dispersal ability, i.e., closer buildings have more similar fungal communities because they are closer to the same fungi, which can’t reach all buildings with equal ease. Important caveat: observed isolation-by-distance is not always due to dispersal limitation. If an important environmental variable is also linked to distance, it could be that variable that is causing more physically distant communities to appear more compositionally different. However, the authors attempted to control for these effects by using buildings that belonged to a single housing unit, made of similar materials and located in close proximity – so the conclusion that it actually is dispersal limitation that is causing the pattern is quite reasonable.

This study is cool to me for a lot of reasons. First, by talking about microbial ecology in terms of dispersal limitation and isolation-by-distance, it helped me get my head around some things and into the micro game. Second, it was very easy to read and I recommend doing that if you’re interested (it’s open access!). Third, I’d never thought about where my home’s fungus comes from and I love that technological advances are facilitating the asking and answering of these types of questions. Hooray for fungal research.

Fungi are an amazingly diverse group. (This one is probably not like the ones found in this study…)

For more information on microbiology of the built environment:

Adams, R., Miletto, M., Taylor, J. & Bruns, T. 2013. Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances. The ISME Journal.

From Sarah: Why are honeycombs hexagonal, anyway?

From Devin: How many papers have you reviewed in the past year? And, more important, how many review requests have you turned down?

From Jeremy: Most U.S. states have pretty lousy state birds. (Everyone who picked Northern Cardinal, I’m looking at you.) Here are suggestions for much better ones.

From Sarah: Here are ten ways your house is like an ant’s. And here are ten cool recent dinosaur discoveries.

And, also from Sarah: a new international study shows that students need sleep.

I think we underestimate the impact of sleep. Our data show that across countries internationally, on average, children who have more sleep achieve higher in maths, science and reading. That is exactly what our data show,” says Chad Minnich, of the TIMSS and PIRLS International Study Center.

From Devin: A new preprint server, bioRxiv, is looking to be the ArXive for the life sciences. (But lots of biologists are starting to use ArXive already.)

… Cold Spring Harbor Laboratory Press is set to test the waters in preprint publishing before the end of the year. The service, called bioRxiv, will be largely modeled after arXiv, with a few additional features to entice life scientists. These include public commenting, room for supplementary information and links to established databases such as GenBank.

From Jeremy: A study tests the quality of plant trait data from public databases by comparing it to new samples.

… the correlation between sampling effort and payoff is still (as usual) high. It may be easier to get traits from a database, but it is not usually better.

So, I’ve already announced this in other venues, but, what the heck: I’m collaborating on a new survey of lesbian, gay, bisexual, and trans* folks working in science, technology, engineering, and mathematics (STEM) fields. If that describes you, my collaborator and I would really like you to answer some questions. It’s all anonymous (unless you volunteer for a followup interview), and it’ll help fill a real gap in our understanding.

I am reliably informed that the monthly round-up of online writing about evolution is available now at DNA Barcoding. Reserve a nice long block of time to peruse the links—this month’s carnival is bigger on the inside.

From Amy: The U.S. Department of Agriculture is looking into unleashing parasitoid wasps to control invasive Asian stinkbugs.

From Devin (@DevinDrown): A cure for the contagious cancer plaguing Tasmanian devil populations may rely on making the cancer cells “visible” to the devils’ own immune systems.

It turns out that [devil facial tumor disease] cells down-regulated genes that are required for antigen processing—ultimately leading to a lack of MHC expression on the outside of the tumor cells. Without that signal from the MHC molecules, the immune system is oblivious to this sinister presence, and the cancer proliferates until it has killed the animal—explaining why this disease has a 100% mortality rate.

From CJ (@cejjenkins): What scares sperm whales? Orcas. But, what, exactly is scared by a moth that looks like a spider?

From Sarah (@SarahMHird): What not to do in the early stages of your academic career. And, if you want to despair for the future of science in the U.S., here’s a depressing article about how Pennsylvania science teachers handle/avoid teaching evolution.

“My approach is to teach the textbook content of Darwinian evolution but modified to explain that data can be interpreted differently dependent upon one’s world view.”

From Jeremy (@JBYoder): Sixteen-year-old sets up a DIY chemistry experiment, gets charged with a felony. There’s a petition you should sign.

A system that values obedience over curiosity isn’t education and it definitely isn’t science. Her expulsion and arrest sends a very clear and striking message to students, especially urban students of color: Don’t try this at home, or school or anywhere. Science exploration is not for you!

John Corvino, the chair of the Philosophy Department at Wayne State University, has recently published a book, What’s Wrong With Homosexuality, which systematically knocks down objections to the equality of LGBTQ folks. He’s been discussing major points from the book in a series of clever and widely-circulated videos, and I just recently discovered that, in an episode about the biological basis of sexual orientation, he talks about that review article proposing a possible epigenetic basis for sexual orientation that I discussed here a few months ago.

Full disclosure: I found Corvino’s post, actually, because he linked to my piece about the epigenetics paper, and he did so while paying it what I consider the highest compliment it’s possible to pay a science blogger: “A nice explanation of the paper can be found here.” Which: look at me blushing.

But Corvino comes at the question from a somewhat different angle than a biologist: he says it really doesn’t matter whether there’s an inborn basis to sexual orientation.

Why are some people so quick to latch on to bold claims about the biological origins of homosexuality? I think it’s because they believe that we need to show that we’re born gay in order to establish that our sexuality is a deep, important and relatively fixed part of who we are. But that’s simply not true. Consider a counterexample: My comprehension of English is a deep, important and relatively fixed part of who I am. I could acquire other languages, of course, but none would subsume my native tongue at this point. Being forbidden to express myself in English would be a real deprivation. But I wasn’t born comprehending English.

I agree with that entirely. The question of whether or not it’s “natural” to be gay doesn’t tell us a damn thing about how society should treat gay people; there are all sorts of elements of modern life that are demonstrably un-natural (in the sense that they’re not what our ancestors did just after they came down from the trees, which I guess is the standard—right, Sarah?), but I think we can all agree it would be absurd and wrong to try and eliminate them from our lives: Antibiotics. Telephones. Creative writing. That game people play with brooms and a big round stone on an ice rink.

But there is something in Corvino’s take on the issue that rubs me the wrong way just a little bit:

It’s also troubling that this paper, like much research in this area, singles out homosexuality as a particular riddle to be solved. It’s as if heterosexuality were the default setting, requiring us to figure out “what went wrong” when people turn out gay.

Well, yes—there certainly are people who think something “went wrong” with queer folks, but I really don’t believe that any of the biologists studying the evolutionary history of sexual orientation are among them. Evolutionary biology is fundamentally interested in variation—differences between species, differences between individuals within species, and how the former arises, over time, from the latter. I want to understand the genetic basis of my sexual orientation for the same reason I want to understand the genetic basis for my continued ability to digest milk sugars decades after I stopped nursing: because the answers to these riddles provide clues about how I came to be the way I am, and how all of humanity came to be the way we are, today.

Does answering that question matter for deciding present political issues like marriage equality? Not so much. But I absolutely believe it’s a worthwhile and enriching pursuit.

Postscript: Here’s the “born this way” episode of Corvino’s series, which—lest you think otherwise from my complaining above—is well worth your viewing time.

Further postscript: I thought about illustrating this post with the obvious music video, but I still have no idea what’s going on for most of it. Mitosis of the what now? And where’s Jimmy Stewart?

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.

In our evolutionary past, small groups of hunter-gatherers needed enforcers, individuals who took it upon themselves to punish slackers and transgressors to maintain group cohesion. We evolved this way. As a result, some people are born to be punishers. They are hard-wired for it.

The giant moray eel can grow to three metres in length and bites its prey with two sets of jaws—the obvious ones and a second set in its throat that can be launched forward like Hollywood’s Alien. It’s not a creature to be trifled with. But the coral grouper not only seeks out giant morays, but actively rouses them by vigorously shaking its body. The move is a call to arms that tells the moray to join the grouper in a hunt.

Smelling like a zombie works out well for the plant known as skunk cabbage. The species is featured on the third full episode of the “Plants are Cool, Too!” video series. Hosted by Dr. Chris Martine (Bucknell University) with special guest Dr. Rachel Schultz (SUNY Plattsburgh), the episode was filmed in the Adirondack Mountain region.

The cancer-targeting microorganism, Listeria monocytogenes, is a rod-shaped bacterium that penetrates the cells of the people and animals that it infects…Because of the bacterium’s ability to burrow inside key immune cells called macrophages, some researchers use weakened Listeria with bits of tumor DNA attached to teach the body’s immune system to recognize and destroy cancerous cells that might otherwise slip by unnoticed.

Although a number of guides exist online, many researchers still feel overwhelmed and hesitant toward the virtual world, lacking sufficient information and guidance through formal scientific channels such as peer-reviewed journals. To better familiarize researchers with existing internet resources, here we discuss prospective benefits that can stem from online science conversations, explain how scientists can efficiently and effectively harness online resources, and provide an overview of popular online tools.