Opening up open access

At a conference a few years ago I spoke with a friend who said “when I talk to people who say “I’m going to publish 5 papers this year, even though I haven’t submitted any” and it’s July I smile inside. It takes so long to publish papers there is no way they will be able to publish 5 by December”. It’s true, it takes forever to publish (after the writing and submitting part, which for me takes awhile too).

But some scientist, even Nobel Prize laureates, are publishing things online before even submitting it for review in an “official” publication. Not only does this cut out the journals who are arguably making a ton of profit off our free labor (see here and here), but it gets your work out to the scientific community faster.

Read about it over at the New York Times! 

from asapbio.org/yourekascience.org

from asapbio.org/yourekascience.org

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Happy Anniversary Planet Earth! Episode 6: Ice Worlds

Both poles of our planet are covered in ice. They are the largest and most demanding wildernesses of all.

Sigh. We’ve made it to the Ice Worlds episode – the one where the changes of the last ten years are most obvious.

Our understanding of climate change has increased greatly in ten years, although many (especially in the US) remain in doubt. The episode begins and ends in the Arctic, where polar bears are the keystone predator and our adopted mascot for efforts to stop climate change. Maybe you’ve seen the super depressing pictures of starving polar bears. Or the pictures of them swimming in open water. Unfortunately, these aren’t the only animals threatened in these habitats – in fact, basically all animals are negatively impacted by climate change.

Long term studies show Adelie penguin and Chinstrap penguin populations are declining. Antarctic sea ice provide fungus for krill to eat, which the penguins survive on. Emperor penguins fare no better, and their populations are expected to decline massively over the next 50 years or so. Humpback whales also feed on krill in the Antarctic and may be starving as the krill populations decline.  Several birds breed in the Antarctic. Climate change affects these birds in many ways – there may be more nesting habitat for these birds, like Snow Petrels, but the birds also seem to be breeding later in the year as sea ice cover timing changes.

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Time for your close up, Ms. Krill.

The sun’s influence diminishes and the ocean starts to freeze. the greatest seasonal change on our planet is underway…

Antarctica is losing ice. This topic has been discussed extensively (see various links here) and is of obvious importance. Unbelievable amounts of ice are doing (nearly) unbelievable things. Weather systems are becoming more dangerous and more costly. What is being done? The White House has enacted some plans for combating climate change and in 2015, the United Nations Climate Change Conference in Paris led to the “Paris Agreement”, outlining a global reduction of climate change (specifically, a limit of global warming and greenhouse gas emissions). These steps are necessary and it’s encouraging that the Paris Agreement has global support. I guess it remains to be seen whether these efforts are enough.

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Ice. It’s pretty. I hope it’s not an endangered species.

Unlike Antarctica, the Arctic is a vast frozen sea surrounded by land.

The same threats and stories are occurring in the Arctic as the Antarctic. Arctic Musk oxen are declining and their range contracting due to climate change as well (and this may have been occurring for the last 10000 years – covered previously at NiB!)

Bad news is everywhere you look when it comes to the Ice Worlds. I’ve watched this episode several times now and it depresses me more each time. Time to focus on getting mad (and proactive) instead of get sad though: here are some tips from the USA Environmental Protection Agency  on how to start combating climate change on a local scale.

The episode ends with more shots of polar bears. I really hope 10 years from now we’re reporting population growth and decreased greenhouse gas emissions, instead of the easier to imagine and much less pleasant alternative.

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Polar bear mama and cub.

Following their mother has prepared them for life at the pole, an ever changing land ruled by ice. Whether they are ready for the bigger changes that have begun to shape the ice worlds of our planet remains to be seen.

The Postdoc

When we started this blog, the majority of the contributors were graduate students. Now, everyone has moved onto other stages in their careers (good job! go team!). But as I was the youngest when we started, I am the only one who remains pre-PhD (but finishing up this spring!).

And as a result, I am thinking about/applying to postdoctoral positions. I have written a bit about the postdoctoral position in the grand scheme of academia (here and here(especially the second post, Jeremy really summed it up excellently)).

And adding to the stack of interesting reading, this post about how a new PI views postdocs and how their plight is viewed from someone recently on the other side.

from PhD comics

from PhD comics

 

Genetic Drift vs. Inbreeding

I got this question as part of my preliminary exam: “What effect does genetic drift have on inbreeding?”

It is a difficult question to answer, and one that I’ve thought on often over the years. So imagine my delight when over at the Molecular Ecologist (If you aren’t reading the Molecular Ecologist every week, you are missing out. Seriously. Go read all of it. Now) Patricia Pecnerova wrote an article addressing the complexities of this very question.

Check it out here. And read all their stuff.

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They are also doing a fundraising campaign, and have a cool logo (see above) which you can get on a tshirt or Mug.

Happy Anniversary, Planet Earth! Episode 5: “Deserts”

As the fifth episode of Planet Earth begins, it feels like you might have stepped onto another planet.

The Namib desert (flickr: mariusz kluzniak)

The Namib desert (flickr: mariusz kluzniak)

Desert landscapes have an alien, otherworldly feel to them; vast swaths of sand around the world have acted as the backdrop for NASA equipment tests, science fiction classics like 2001: A Space Odyssey, and, of course, supposed extraterrestrial activity. But despite their interstellar associations, deserts are very much of this planet. As narrator David Attenborough tells us, deserts cover a third of the Earth’s surface, and all of them are populated with life.

“Deserts” takes us into a world of extremes, where the environment can go from habitable to hostile in an instant. In this 10-year anniversary post we will relive the episode’s most intense moments, highlighting the incredible challenges that accompany life in Earth’s driest places. We will also take a look at the unique difficulties conservationists face in attempting to protect the organisms that inhabit these inhospitable regions.

Desert Survival is About Timing

In the deserts of our planet, extremes are the norm. Attenborough tells us that temperatures fluctuate annually in the Gobi Desert from -40° C in the winter to 50° C in the summer. Death Valley holds the record for highest temperature ever recorded, at 56.7° C. In the Sahara Desert, sandstorms to rival Mad Max can reduce visibility over regions the size of Great Britain for several days, and the resulting dust clouds can affect weather patterns around the world.

Things don’t happen in moderation here.

Good conditions are transient, and when they do occur, organisms must be ready to take full advantage of them. Timing is everything when you are trying to survive in the desert, a fact that is apparent in multiple segments of the “Deserts” episode. Kangaroos in Australia forage in the early morning when temperatures are moderate, but must find a tree that provides suitable shade from the sun before midday, lest they risk overheating. Scorpions and toads in the Sahara have almost no tolerance for the sun’s rays, and must emerge from shelter only at night.

The importance of timing shows up in somewhat unexpected ways as well. For example, wild camels have fine-tuned the timing of their breeding season to coincide with the onset of winter, when precipitation is the most abundant. In the Gobi Desert, snow covers the ground throughout the winter months, providing a reliable and widespread source of water for the camels. Planet Earth camera crews searched the Gobi for two months for these rare and elusive animals, finally obtaining fantastic footage of the bizarre mating rituals of the species.

The ephemeral nature of favorable conditions means that a single bout of resource availability must sustain desert plants and animals for long periods of time. In Namibia, a flash flood (one of just a handful that occur annually) produces a burst of vegetation growth. This rare resource attracts oryx to area, which in turn attract a family of lions. Attenborough tells us that a single oryx will sustain the entire lion family for a week. These infrequent bouts of productivity are key in maintaining life here, for a range of species.

Rain is also infrequent in the Sonoran Desert. Consequently, the saguaro cactus is well-adapted to make the most of the brief Arizona monsoon season. The pleats on its trunk allow the cactus to expand, so that it can absorb as much of this valuable resource as possible- up to 5 tons! And if the cactus is good at collecting water, it’s even better at making it last; it can live off these stores through multiple months of drought.

A saguaro cactus (flickr: Michael Wilson)

A saguaro cactus (flickr: Michael Wilson)

When resources like water are so difficult to come by, one survival strategy utilized by many desert species is to rely on other organisms collect them first. In the Atacama, the only predictable source of water comes in the form of a fog generated by cold ocean currents. Coastal communities of plants called lomas collect the fog’s moisture, and provide life-sustaining hydration for a number of desert organisms. Guanacos eat cactus flowers for the water they contain, and coyotes lick dew off of moisture-loving lichens.

Interacting with other species can also be key if you are a traveler, trying to get across the depauperate desert environment as quickly as possible. For just four weeks during the summer, saguaro cacti bloom during the night. The timing of this event corresponds to the annual migration of the lesser long nosed bat. As bats travel across the Sonoran during their trip from Mexico to the United States, they subsist on nectar from the flowers, fertilizing the next generation of cacti along the way. The bats would have no hope of making it across if it wasn’t for this short-lived food source, and the saguaros in turn rely the bats for pollination.

While resources are fleeting in the desert, we learn that some elements of this ecosystem stick around for a surprisingly long time. For instance, star dunes in Namibia can reach up to 300 meters high. The sand at the peaks of these dunes is in almost constant motion thanks to the wind, but sand at the base may not have shifted for 5,000 years. In addition, locust eggs lie dormant for 20 years before they hatch, and seeds in Death Valley can wait for 30 years for favorable conditions before they sprout. A “superbloom” of wildflowers is currently taking place in Death Valley- what a fantastic way to celebrate the anniversary of Planet Earth!

The Curious World of Desert Conservation

In the desert ecosystem, organisms face a somewhat bizarre set of conservation challenges.

From the illicit underground cactus trade, to the legacy of nuclear weapons testing; from rabbits run amok in Australia, to the controversially brutal hemorrhagic disease released to control them; from a history of violent confrontations between the federal government and armed ranchers, to the endangered desert tortoise that first set those land disputes in motion- conservation in the desert has a strange and dramatic past.

In terms of scale, The Great Green Wall of Africa is as dramatic as conservation comes. An effort to counteract the ongoing effects of desertification, the Great Green Wall project proposes to plant a corridor of drought resistant trees along the southern edge of the Sahara. The Great Green Wall, if completed, will be really, really long: 4,750 mile long and 9 miles wide, to be exact. It’s a huge undertaking, with 12 nations currently in collaboration on the project. But if all goes to plan, the Great Green Wall will be quite an amazing feat of conservation.

Big game hunting presents another dramatic desert conservation issue. In 2014, Namibia issued a handful of licenses to hunt desert elephants. Desert elephants are distinct from African elephants, exhibiting a number of behavioral and morphological adaptations for desert life. These locally adapted animals are also exceedingly rare, with fewer than 100 individuals in Namibia. However, desert and African elephants are not technically considered separate species, and thus the Namibian government does not currently extend any additional protection to these populations. This controversy highlights the importance of species delimitation in conservation- an issue that is only more dramatic in the context of big game hunting.

A desert elephant (flickr: Vernon Swanepoel)

A desert elephant (flickr: Vernon Swanepoel)

The plants and animals of the desert are some of the planet’s most hardy, but even they can have difficulty rebounding from disturbance. In the Atacama, the life-sustaining lomas are at risk. Local people rely on the water-collecting capabilities of these plants for survival, but have also destroyed the majority of the vegetation to make way for agriculture. Researchers are attempting to replant one particular plant, called the tara tree, in hopes that it will help to rehabilitate these important communities. But new seedlings seem to have trouble taking hold within existing lomas. Lomas are home to 1,400 plant species, around half of which are endemic; their loss would be truly devastating to the region.

Deserts, with their reputation as barren wastelands, may not seem like obvious targets of conservation. Desert flora and fauna face extreme conditions on an everyday basis, and the added strain of human impacts makes survival all the more difficult for these organisms. But on the bright side, evidence suggests that our effects on deserts can be successfully mitigated. In the case of the once-threatened Eureka dune grass, limiting the use of off-road vehicles in particular regions of Death Valley has been enough to allow populations of the plant to reestablish.

Life in this unique desert ecosystem defies all odds, and protective measures will be key for helping it to persist into the future.

Be sure to stick with us as we continue our celebration of Planet Earth’s 10-year anniversary! Check out our posts on “From Pole to Pole,” “Mountains,” “Fresh Water,” and “Caves.” Next week we’ll be looking at the polar opposite of deserts: ice worlds!

 

The Tully Monster

In 1955 Francis Tully found a fossil 50 miles south of Chicago that looked like “an obese foot-long earthworm with a trunk and a spade shaped tail”. See below.

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When Mr Tully brought his discovery to the field museum, where they had no idea what it was either (but they named it Tullimostrum gregarium, which is latin for “Tully Monster”). Or what it might be related to. Or what animal group it belonged in. What they did know was that this strange monster wasn’t rare, in fact specimens started cropping up all over the place.

50 years, and 1200 specimens later, Victoria McCoy and a team of scientist have solved this very puzzling mystery. Read about it over at the Atlantic, or the original paper here.

The insignificance of the significant pvalue

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p<0.05

We’re told early and often that this means that your data is significant. But statisticians and biologists that are statistically inclined, while tell you (and have been telling us for awhile) that this is a completely arbitrary figure. Like most tools, in statistics if you use the pvalue incorrectly you’re doing yourself and your science a disservice.

And the American Statistics Association agreed, and disagreed. Last week they released an AWESOME statement on p-values.

Read the original, or the equally excellent synopsis over at the Molecular Ecologist (I can’t give that blog enough love…)

xkcd comics

xkcd comics