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: Safer sex is also good for the environment, as endangered species condoms will remind you.

The Center for Biological Diversity marked this year’s Earth Day by distributing 100,000 free Endangered Species Condoms around the country. The Center collaborated with artist Roger Peet to create special editions of the colorful condom packages featuring a suite of species — from the dwarf seahorse to the polar bear — threatened by the world’s growing human population.

From Devin: The inside scoop on NIH grant review.

During each meeting, Council members review more than 1,000 applications. While they do not discuss the vast majority of them, they must vote whether to concur with the study section recommendations. For most applications, this is done en bloc.

From C.J.: The last Pinta Island giant tortoise, Lonsome George, died this week.

The rarest animal in the world is no more. Lonesome George, the last of the Pinta Island tortoises, was found dead on Sunday. But a small hope remains for his subspecies, as its genes have survived.

“He was an iconic animal for the Galápagos,” says Robert Silbermann, chief executive of the Galapagos Conservation Trust.

And from Jeremy: In tomatoes, the same receptor protein activates defensive responses against both leaf fungus and root worms.

We found that the extracellular plant immune receptor protein Cf-2 of the red currant tomato (Solanum pimpinellifolium) has acquired dual resistance specificity by sensing perturbations in a common virulence target of two independently evolved effectors of a fungus and a nematode. The Cf-2 protein, originally identified as a monospecific immune receptor for the leaf mold fungus Cladosporium fulvum, also mediates disease resistance to the root parasitic nematode Globodera rostochiensis pathotype Ro1-Mierenbos.

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: Bears understand numbers! (See also Jason Goldman’s in-depth discussion of this study.)

The experiment then involved presenting the bears with two sets of dots or “arrays”.

“Basically we were looking to see if they can understand to choose less or choose more,” she said.

They touched the screen to select one or other of the arrays, and were given food if they got the answer right.

And from Jeremy: Even though virologists now know a lot about the pandemic potential of H5N1 influenza, there are some important questions remaining.
“What is so special about this virus that allows it to spread through the animal world so effectively?” asks Jeremy Farrar, a tropical-medicine specialist at the University of Oxford, UK. There are no firm answers.

#Evol2012: Preparations

The Ottawa skyline.

The Evolution 2012 meetings (more formally, the First Joint Congress on Evolutionary Biology) is almost upon us. From 6 to 10 July, members of the American Society of Naturalists, the Society of Systematic Biologists, and the Society for the Study of Evolution (three North American professional societies that usually meet jointly) will join the Canadian Society for Ecology and Evolution and the European Society for Evolutionary Biology in Ottawa for what will be pretty much the biggest meeting of evolutionary biologists ever.

And we’re going to be there! Many of the contributors to Nothing in Biology Makes Sense! are giving talks. From the program [PDF]:

  • Noah Reid: “Do multi‐species coalescent models fit empirical data?” in the SSB Symposium on Saturday at 9:30 am, in room 214
  • Devin Drown: “Evolution of transmission mode in obligate symbionts,” in the Evolutionary Theory 1 concurrent session on Monday at 1:45 pm, in room 206
  • Sarah Hird: “Using gut microbial fingerprints to explore ecology and evolution in Neotropical birds,” in the Phylogeography 7 concurrent session on Monday at 1:45 pm, in room 210
  • C.J. Jenkins: “Evaluating the Importance of sexual reproduction vs. ploidy in the face of a coevolving parasite,” in in the Evolutionary Theory 1 concurrent session on Monday at 2 pm, in room 206
  • Jeremy Yoder: “Genome‐wide footprints of local adaptation to habitat in Medicago truncatula,” in the concurrent session Ecological Genetics 11 on Tuesday at 9:45 am, in room 205

(Sarah and Devin will have to fight it out over that scheduling conflict. I propose arm-wrestling.)

In the next couple weeks, we’ll also be posting about sessions that we’re looking forward to. We’re also going to be posting from the conference, of course, highlighting all the coolest new science on the subject of descent with modification.

The official blog for the meeting has been providing some handy resources for those of us who aren’t familiar with Ottawa, including a list of pubs, and information about the city-wide bike sharing program. Over at the Oikos blog, Jeremy Fox has created an annotated map of recommended places to eat and drink. And there’s an officially-selected Twitter hashtag to follow, too: #Evol2012.

What’s changed in evolution and ecology since I started my Ph.D.

The rise of big data is changing ecology and evolutionary biology, along with the rest of the life sciences.

This week’s post is a guest contribution by David Hembry, who recently finished his Ph.D. at the University of California, Berkeley, working on coevolution and diversification of the obligate pollination mutualism between leafflower plants (Phyllantheae) and leafflower moths (Epicephala). He will be starting a postdoctoral fellowship at Kyoto University in the fall.

Last month, I filed my PhD dissertation, bringing to an end an intellectual and personal journey that began seven years ago in the summer of 2005. I know a lot more now than I did then, and I know a lot more about the boundaries of what I don’t know, too. But not only has my knowledge changed—evolution and ecology looks a lot different now than it did seven years ago when I was planning my dissertation research. At some point, and often multiple points, in the process of getting a PhD, everybody wonders whether what they’re doing is already out of date. 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. Looking back, and looking towards the future, here are the changes I think were most important (from an evolutionist’s perspective), and what I think they mean for young scientists.

Continue reading

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 Devin: Do big sporting events create big opportunities for infectious disease transmission? Depends on the event.
Even those who make a living studying mass events say the risks shouldn’t be exaggerated. But outbreaks do happen, even at sports events in rich countries, Khan says; there was an outbreak of leptospirosis among triathlon athletes in 1998 in Illinois, for instance, and a cluster of meningitis cases was linked to a rugby match in the United Kingdom. What’s more, studies may miss some cases if they become apparent only after spectators go home. That might be especially true for diseases like tuberculosis, which can lie dormant for years.
From Jon: A “vaccine” for Parkinson’s Disease is starting human trials.

Called PD01A, the drug primes the body’s immune system to destroy alpha-synuclein, a protein thought to trigger the disease by accumulating in the brain and disrupting dopamine production.

Affiris, the company in Vienna, Austria, that developed the vaccine, says it is the first treatment to target the cause of the disease.

And from Jeremy: Blogging scientist Gerty-Z goes to an NIH study section, and reports on the grant review process from inside the metaphorical lion’s den. (Part 1; part 2.)

It was surprisingly hard to give out bad scores! But I do what I gotta do. For each of my grants, I did some literature searches and read up so that I had an understanding of the field. Obviously, all of the grants were in my Field, but some were outside of my own sub-field expertise. This was important to help me figure out what the “impact” of the research might be [HINT: spell out what the “impact” will be when you are writing a grant!!!!] In addition to “my” grants, I read the Aims page of all the grants we would be reviewing (THIS IS WHY YOUR AIMS PAGE IS SO IMPORTANT).

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: Have humans pushed the planetary environment headed toward a “tipping point” of rapid change? Very possibly.
“Everything that happened the last time around is happening now, only more of it,” said [UC Berkelely paleoecologist Anthony] Barnosky of the last ice age’s end and ongoing changes to Earth’s climate and biosphere. “I think the evidence makes it pretty clear that another critical transition or tipping point is very plausible within the next century.”
From CJ: America’s “brainiest” cities, calculated. Well, okay, then:
5. San Francisco-Oakland-San Jose
6. Cedar Rapids-Waterloo-Iowa City & Dubuque, Iowa
7. Honolulu
8. Johnstown-Altoona, Pennsylvania
9. Champaign & Springfield-Decatur, Illinois
10. Minneapolis-St. Paul
11. Boston-Manchester (Massachusetts/New Hampshire)
12. Austin
13. Rochester, New York
And from Noah: Video of a cockroach’s preferred method of escape, which has inspired robot design.

Carnival of Evolution, June 2012

The monthly roundup of evolution-related online writing is (finally) live at Pharyngula, now that host P.Z. Myers is back from a trip to Iceland. P.Z. indulges his hominid cognitive biases by sorting the contributed links into neat, if somewhat idiosyncratic, categories: Bacteria, Plants, Charismatic Megafauna, Humans, Charismatic Organs in Charismatic Megafauna (i.e., mostly brains and penises), Theory, History, and Idiots. Take a moment to speculate as to where our own contributions were classified, and then head over to the Carnival for posts from Jerry Coyne, Anne GutmannArvind Pillai, and many more.

Use it or lose it?

This post is a guest contribution by Dr. Levi Morran, NIH postdoctoral fellow at Indiana University. Levi studies the role that both coevolutionary relationships and mating systems play in shaping evolutionary trajectories. His research using experimental coevolution to test the Red Queen hypothesis recently appeared in Science and was featured on NPR and the BBC.

The 40 Year-Old Virgin movie poster

The 40 Year-Old Virgin

In the movie, The 40 Year Old Virgin, Steve Carell’s character (the title character) asks a sex education instructor, “Is it true that if you don’t use it, you lose it?” Given the context, I’ll allow you to put the pieces together and figure out just what he was referencing with the question. But, the phrase “use it or lose it” is quite catchy isn’t it?

Surprisingly, the phrase is thought to have some relevance in the field of evolutionary genetics, particularly regarding bacterial genomes. You see, widespread gene loss and genome reduction has been observed in some strains of bacteria, particularly those that specialize in certain environments (Cramer et al. 2011; Ernst et al. 2003; Smith et al. 2006). But, how and why do bacteria “lose it”, and do they lose it because they don’t use it?

Continue reading

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: Many of the biggest names in field botany are getting close to retirement, and it’s not clear who will replace their expertise.

As the star collectors disappear, botanists are debating how to fill the gap. Some researchers, including Wood, are training botanists in tropical countries, the presumed home of most undiscovered plants. But others think that it might be more efficient to recruit a large group of less-skilled collectors, aided by technology and crowdsourcing techniques. “The real question is, can we exchange a few elite collectors for an army of enthusiastic less-experienced collectors?” asks Cam Webb, a Harvard University plant scientist based in Indonesian Borneo.

From Jeremy: A new study of flowering time variation in Arabidopsis makes clever use of ecological niche modeling.

While this period of early growth has tarnished some people’s view of ENMs, it would be a shame to disregard them altogether when there are people still using them in interesting and inventive ways. A great example is Banta et al. (2012), which combines a model organism, intraspecific phenotypic variation, and spatial structure of genetic variation with ecological niche modelling. Banta et al. focus on the problematic assumption of such models that intraspecific variation in climatic tolerances is minimal or unimportant. One approach to exploring this issue more is to develop intraspecific ENMs using genotypes, rather than species, as the unit of analysis.

From Jon: Is Chagas disease “the new HIV/AIDS”?

Neglected tropical diseases (NTDs) are among the most common conditions afflicting the estimated 99 million people who live on less than US$2 per day in the Latin American and Caribbean (LAC) region [1]. Almost all of the “bottom 100 million” living in the Americas suffer from at least one NTD [1], and according to some estimates, the NTDs cause a burden of disease in the LAC region that closely approximates or even exceeds that resulting from HIV/AIDS [2]. Chagas disease (American trypanosomiasis) is a vector-borne disease and a leading cause of the deaths and disability-adjusted life years (DALYs) lost that result from NTDs in the LAC region [2]. With approximately 10 million people living with Chagas disease, this condition is one of the most common NTDs affecting the bottom 100 million in the region, a prevalence exceeded only by hookworm and other soil-transmitted helminth infections [1][2]. Moreover, among the NTDs in the Americas, Chagas disease ranks near the top in terms of annual deaths and DALYs lost [1][2]. [In-text citations sic.]

From Devin: Should be extending the Modern Synthesis? Dickins and Rahman (2012) write a very strong and clear argument against the Extened Evolutionary Synthesis as proposed by Pigliucci and colleagues.